Overview
These are my personal tweaks to Fallout 4 perks to make my ironman (no reloading, you die and you're dead) playthroughs more fun and less annoying. Some perks are slightly weakened, some are slightly strengthened, some are just made more "symmetrical" and some are merged to make room for new lore-friendly perks. I created them based on my past experience and they may require more testing; any feedback regarding balance or anything else is welcome. (That doesn't mean I will make changes and adjustments on demand, though, unless I really like the idea.) This sort of thing is very reliant on personal preference so the changes are uploaded in separate modules. Everyone can download or ignore any combination they like - in case you want a single file, there is a merged and largely expanded version here. Currently available are these esp files:
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Demolition Expert
L00: Duck and cover! Your explosives do 25% more damage, you can craft explosives at any Chemistry Station, and you can properly cover yourself reducing damage from explosives by 20%.
L10: Your explosives now do 50% more damage, you take 40% less damage from explosives and grenades gain a throwing arc.
L22: Your explosives now do 75% more damage and affect a larger area, you take 60% less damage from explosives.
L34: Your explosives now do double damage. Mines and grenades shot in V.A.T.S. explode for double damage, too. You take 80% less damage from explosives.
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Summary: Oh, explosions! The greatest dread in ironman playthroughs (at least for me and my brother :-D). Since real-life demolition experts prefer protecting themselves to causing more damage. At first I considered just replacing the increased explosion damage by player with explosion damage reduction but I felt it wouldn't affect the gameplay in a good way, so I simply buffed the perk in the end. Given how unforgiving ironman-style Survival difficulty Fallout4 is, I figured it would't be so bad.
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Adamantium Skeleton
L00: Your skeleton has been infused with indestructible metal, reducing limb damage and fall damage by 30%.
L13: Your limb damage and fall damage are now reduced by 60%.
L26: Your limb damage is completely eliminated and you take no damage from falls.
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Summary: Not very useful perk in vanilla for me. Crippling is less common than in FO3/FNV and since you can heal it simply by using a stimpak (which you would probably use anyway because crippling effects also damage you), there is little reason to invest 3 perk points here just to gain limb damage immunity. However, since adamantium bones do not break from swatter hits, why would they break from falls? Fall damage elimination at 3rd rank is hardly overpowered considering that just wearing power armor grants you the very same effect or that a certain perk completely prevents death by drowning at its first rank.
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Awareness
L00: To defeat your enemies, know their weaknesses! You can view a target's specific damage resistances in V.A.T.S.
L04: To defeat your enemies, know where they are! Stay still while crouched to detect nearby life forms.
L08: To defeat your enemies, keep track of them! Sighted aiming marks enemies with a compass pip.
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Summary: Vanilla awareness is useless. Sure, it was neat while playing FO4 for the first time when you might have had no idea about enemies' resistances but if you have played FO4 at least half as much as I have, you now remember strengths and weaknesses by heart and there is absolutely no reason to invest a perk point here. That's why I added 2 more ranks which grant you the tracking and detecting effects - they fit the Awareness perk nicely and provide an alternative way to get those effects if you are not into crafting.
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Big Leagues
L00: Swing for the fences! Do 20% more melee weapon damage.
L07: You now do 40% more melee weapon damage and gain a chance to disarm your opponent.
L15: You now do 60% more melee weapon damage and gain an increased chance to disarm your opponent.
L27: You now do 80% more melee weapon damage and hit all targets in front of you. V.A.T.S. melee distance is increased significantly.
L42: You now do double damage with a melee weapon, gain a chance to cripple your opponent, or grand slam their head clean off, and V.A.T.S. melee distance is increased even more, and the farther the Blitz distance, the greater the damage.
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Moving Target
L00: They can't hurt what they can't hit! Get +20 Damage Resistance and +20 Energy Resistance when you're sprinting.
L24: You now get +40 Damage Resistance and +40 Energy Resistance when you're sprinting.
L44: You now get +60 Damage Resistance and +60 Energy Resistance when you're sprinting.
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Sprinter (Blitz)
L00: On your marks, get set, go! Sprinting costs 20% fewer Action Points.
L12: Sprinting costs 40% fewer Action Points.
L29: Sprinting costs 60% fewer Action Points.
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Summary: Blitz was cool but it felt too "narrow" for me. You have to invest heavily in agility to get it but you are also somewhat forced to invest in strength as well to use it effectively. Besides, the Vault-boy in the perk poster is just running, not blitzing. :-D I merged Blitz's effects into the final 2 ranks of Big Leagues, thus making room for the Sprinter perk which reduces the sprinting cost. This (naturally) lead me to removing this effect from the final rank of the Moving Target perk, it now grant additional resistances instead.
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Vulture (Cannibal)
L00: Feast on mortal flesh to heal your wounds! Eating non-humanoid corpses restores Health.
L19: Eating Human, Ghoul or Super Mutant corpses restores Health.
L38: Eating corpses now restores a significant amount of Health.
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Summary: Pretty self-explanatory. The first rank allows you to eat the corpses of most non-humanoid creatures instead of eating human corpses which is now unlocked by the second rank alongside Ghouls and Super Mutants.
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Ghoulish
L00: Sure, you're still human - on the outside! Radiation now regenerates your lost Health and you slowly absorb contained radiation.
L24: Radiation now regenerates even more of your lost Health and you absorb contained radiation slightly faster.
L48: Radiation now regenerates even more of your lost Health and you absorb contained radiation faster. Also, some Feral Ghouls may randomly become friendly.
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Summary: Ghoulish is underwhelming, reducing radiation is usually much more beneficial than restoring a fraction of health at the cost preventing you to restore the rest of it. It may save your life in battle from time to time but it is too situational. I kept the original effects and added a modest passive rads absorbtion. I know there are already mods out there that do a similar thing but even the weakest of their versions are too strong for my taste. The 3rd rank's absorbtion effect magnitude is equivalent to the 2nd rank of the Solar Powered perk - the first two are at 30% and 60% of that value, respectively. ...and before someone asks, I tried to make it so that the perk actually turns you into a ghoul but the results were less than satisfactory. :-D 
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Lone Wanderer
L00: Who needs friends, anyway? While adventuring without a companion, you deal 10% more damage, take 10% less damage and your carry weight is increased by 15.
L17: While adventuring without a companion, you deal 20% more damage, take 20% less damage and your carry weight is increased by 30.
L40: While adventuring without a companion, you deal 30% more damage, take 30% less damage and your carry weight is increased by 45.
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Summary: Just made it more "symmetric", as I call it, the resulting effects at rank 3 are more or less the same with the exception of the carry weight effect which was reduced to better fit with the Survival difficulty.
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Robotics Expert
-Vanilla Effects-
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Summary: Basically just "unpatched" version which restores the option to hack remotely. It is powerful but fun and makes the perk actually worth it (there is NO WAY I can get close enough to an angry sentry bot without it tearing me to pieces. :-D). I was considering a requirement for remote access, though, something like at least 6 perception or the Hacker perk. Feel free to share your opinion.
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Ironfisted Basher (Iron Fist)
L00: Bash'em with your bare hands! Or with whatever's in them... Unarmed attacks and gun bashing do 20% more damage to your opponent.
L09: Unarmed attacks and gun bashing now do 40% more damage and can disarm your opponent.
L18: Unarmed attacks and gun bashing now do 60% more damage. Bashing and unarmed Power Attacks have a chance to cripple one of your opponent's limbs.
L31: Unarmed attacks and gun bashing now do 80% more damage. Bashing and unarmed Power Attacks have an increased chance to cripple one of your opponent's limbs. 
L46: Unarmed attacks and gun bashing now do double damage. Bashing can now cause critical hits and unarmed criticals in V.A.T.S. will paralyze your opponent. 
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Shotgun Surgeon (Basher)
L00: Take your shotgun and don't let the recoil stagger you! Your shotguns do 20% more damage.
L07: Your shotguns now do 40% more damage and gain a chance to stagger opponents.
L15: Your shotguns now do 60% more damage and gain an increased chance to stagger opponents.
L27: Your shotguns now do 80% more damage and gain a chance to knock down opponents.
L42: Your shotguns now do double damage and gain an increased chance to knock down opponents.
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Summary: Rifleman is also edited to prevent shotguns from getting a damage bonus from it but it remains the same otherwise. The bashing mechanic is a neat addition to Fallout but its perk being at the 8th tier (why for Moira Brown's sake?) of Strength has always forced me to not invest in it. Besides, the Vault-boy in the perk poster is not bashing, he is showing us his shotgun he wants to use to do some mess. :-D Shotguns not having their own perk was also a disappointment. They are treated as rifles and while it is the most reasonable solution, it is not without flaws. "Keep your distance long and your kill-count high." says the Rifleman perk but shotguns are the exact opposite, meant to be used at close-range combat. The result? The Basher perk has been merged with Iron Fist to create the Ironfisted Basher perk and Shotgun Surgeon takes Basher's place.
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Strong Back
L00: What are you, part pack mule? Gain +15 to carry weight.
L10: You now have +30 to carry weight. Having that huge selection of junk on you finally pays off - while overencumbered, you get better selling prices at vendors.
L20: You now have +45 to carry weight. When overencumbered, you can use Action Points to run.
L30: You now have +60 to carry weight. When overencumbered, you can travel without penalties.
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Summary: Again, just made it a bit more "symmetric". I didn't like the 2nd rank not having an extra effect so I created one working while overencumbered - just like the following 2 ranks.
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Explorer (V.A.N.S.)
L00: Let Vault-Tec Assisted Navigational System guide your explorations! The path to your closest quest target is displayed in V.A.T.S.
L04: Experience gained from discovering locations is tripled.
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Summary: A case similar to Awareness so I once again added an extra rank with an extra effect. Probably not as tempting as the extra ranks of Awareness but still might be useful early game.
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Lead Belly
L00: Your entire metabolism has adjusted to the weirdness of the Wasteland! You gain +10 Poison Resistance and take less radiation from eating or drinking.
L06: You now have +20 Poison Resistance and take even less radiation from eating or drinking.
L17: You now have +30 Damage Resistance and you take no radiation from eating or drinking.
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Summary: Lack of reliably accessible ways to increase Poison Resistance was worrisome. It makes sense (kinda) that your metabolism will be able to handle poisons better if it can swallow radiation.
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Animal Friend
L00: Commune with beasts! You will no longer get attacked by wild animals.
L12: Animals will now come to your aid but not against other animals.
L28: You can command animals and give them specific commands.
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Summary: Tame animals by pointing yor gun at them? REALLY? It looks like Bethesda fell in love with the pacify concept at the last minute and decided everything should use it - even though vanilla pacify script is a mess. I have already uploaded a separate mod (Pacify Perks Revised) that fixes and adjusts it the vanilla style but it's not good enough for me, so I restored the F3/FNV version of the perk where first rank makes animals neutral towards you and second makes them friendly. It wasn't hard since it was all in the game already but, like I said, Bethesda obviously replaced it with the pacify system at the last minute. The third rank stays mostly the same except for some condition checks and allows you to command (now friendly) animals.
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Summary: Normal food satiates even after eating a corpse. Strength, Endurance and Charisma are reduced by 1, instead.