I took a fairly different approach to balancing level progression in Fallout 4 than most. I looked at how Fallout 4 works, and it is closer to a traditional RPG. You level up and get more health, better equipment, do more damage, gain skills to approach obstacles differently. What I think most experienced with the vanilla game is that the pieces didn't match up quite right and so game play felt "off". I will try to explain my approach here and then explain why I think other approaches are harder to get right.
So my approach was to look at all of the elements of the game that Bethesda created, that affect level progression, and adjust them to work better with each other. I chose to use player/NPC health as the control and balance everything against that. This means that damage output, healing sources and gear need to become available to the player at appropriate times.
Weapons that do more damage might not show up until later levels, and NPCs who spawn with those weapons won't spawn with higher level weapon mods until even later. This means that NPC damage output against the player will increase at a more gradual rate so that they do an appropriate percentage of damage against the player's health when they hit.
Perks that increase weapon damage, or allow weapon crafting, will not be available until later levels for the same reasons. Those perks and weapon mods need to increase a weapon's damage enough so that the damage output scales with the increased health of NPCs. If they are unlocked too early, it just makes it easier to kill enemies.
Ammunition needs to be scarce for weapons that do extremely high damage so that they are primarily used for high health NPCs (like bosses and large creatures). As an ammo type does less damage, it needs to become more common to allow auto fire as an option. Health items need to become more common/powerful later in the game as you face tougher opponents.
Legendary items add to player progression as well. The more you collect, the stronger you become (and the higher the chance you will get something useful to your build). I chose to reduce the rate at which players receive them to slow this process.
Armor also needs to be tweaked so that the player can't become near invincible and you get appropriate protection at an appropriate level.
Side Perks need to be factored in as well. Perks that increase healing, health or damage output in interesting ways like Ghoulish, Solar Powered or Bloody Mess all contribute to the player's power creep. These need to be beneficial enough to tempt players, but not so powerful that they reduce challenge and make the game less exciting. And if these types of perks are ignored they can easily throw off the rest of a balance mod.
A popular method of rebalancing Fallout 4 is to change it to a flat health system. As you level up, your health and the health of NPCs changes very little. The problem with this for me is that everything Bethesda has created has been designed against this. So you need to make much more drastic changes to the systems I mentioned above for this to work. That's not to say it can't be done (some people have done impressive work making overhauls of this type). I just chose my approach as it was more in line with what I had hoped Fallout 4 would have been like on release.
Realistic Weapon Balance
I've seen a lot of weapon overhauls attempt to focus on realism with weapons. Basing stats of weapons on real world expectations. The issue here becomes whether or not these changes work with the rest of the games progression systems. If a weapon now performs better or worse, does it show up earlier or later in the game? If this type of ammo does more damage, is it harder to acquire? If you've made automatic weapons do as much damage per shot as single fire, why would you use single fire? This can be an interesting approach for those wishing to make the game feel more like a mil-sim. But again it's tricky to get right within an RPG progression system.
This is the idea to make all weapons balanced against each other. Similar to a classic Multiplayer Deathmatch Arena. A pipe rife might perform differently from say a combat rifle, but from a technical standpoint their differences balance out. This is an interesting idea, and I suppose the appeal is that nothing becomes obsolete. I think if done right this can be interesting. Unlocking new weapons would feel more like unlocking a new gun for loadouts in a Battlefield or Call of Duty game.
I think this is mostly a matter of taste. There are a decent amount of perk overhauls out there and some have come up with interesting ways to improve balance or make gameplay more fun. I don't think I've found a set that I 100% like and I'm sure many will say the same for what changes I've made (myself included). There are just a lot of limitations modders have to work around to come up with solutions to issues due to how the perk chart is designed.
Novelty vs Need
I think this is a big one, and a trap I find myself falling into on occasion. It's adding something to the game just for the sake of it, rather than because an area of the game feels lacking in some way. Let's look a my changes to food in the game. I locked cooking recipes behind ranks of Lead Belly based on how useful those foods were. But now that each rank unlocked recipes, I felt I needed to add new foods to make each perk rank worth taking. The top rank unlocked recipes for foods that buffed SPECIAL stats, but only a few foods buffed a few SPECIAL stats. So the need arose to make sure that there was one food type per SPECIAL stat. I could have just made 30 new food types to say that I had done so, but instead I just added what I felt would balance out the new system of unlocking higher quality recipes.
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