Pairing Improved Atmosphere (or FCR alone) with the latest QUDAO fixpack results in broken quests and other bugs, so I made FCR compatible with the latter. Main package makes FCR compatible with QUDAO and removes IA stuff from FCR (and isn't fully compatible with IA). Miscellaneous package only removes IA stuff from FCR (just in case anyone ever needs this). I have no idea how much of the Improved Atmosphere mod can be used with this, but, in my opinion,  it's rather pointless to try it, because the main draw of that mod for me is the set of area changes, which get negated by this patch for the sake of compatibility with QUDAO. This was made with QUDAO fixpack v3.52 in mind.
I did a full playthrough of the game and all origins with this and didn't encounter any mistakes.
Below you will find a full installation guide. You don't need to follow any other mod's installation instructions. Do read their descriptions to have some understanding. I recommend using DAO modmanager.

Notable differences from FCR:
Lowered the ranks of Paedan's "co-workers" and (most of) Cauthrien's lackeys, because they didn't make sense and were a bit too difficult.
Lowered the ranks of generic werewolves, because the werewolf lair was way more difficult than other content. Their ranks are pretty much vanilla now (normal by vanilla naming, hard by FCR naming).
Lowered the ranks of shades in a random shade encounter.
Some other minor changes not worth mentioning.

I also added two creature files for ranged soldiers in Denerim stealing encounters, which should prevent them from getting Scattershot and deleting your party with it. This is a small tweak on the vanilla game. These files are already included into the package (dencr_gen_soldier_bow.utc and dencr_gen_soldier_cbow.utc). With this and some minor rank adjustments, early game should be smooth regardless of what you run into.

Installation:
1. Install FCR into "\Documents\Bioware\Dragon Age\packages\core\override", only "1. Ranks" folder is needed;
1.1 (Optional) Keep some of the files in "2. Difficulty" folder:

• APR_base_FCR.gda — removes enemy max level caps;
• difficulty_FCR.gda — reduces healing efficiency to 25% on nightmare difficulty. I don't recommend this;
• packages_base_FCR.gda — enemy levels per skill ratio set to 1 (was 1.8 to 6). You'll see much more variety in abilities being used. Freshens up
  the game a bit, but makes it more difficult in places;
• autoscale_FCR_*.gda — rebalance of enemy stats. You need only one of these, or none. The biggest difference is between Normal autoscale and
  none, and that difference is huge. It increases enemy HP among other things. "Normal" autoscale file with normal difficulty setting in-game is noticeably harder than vanilla Nightmare. Only the Very Hard file turns One-Hit-Kill darkspawn into normal (hard by FCR naming) darkspawn. Optional download on this mod page has Vanilla, Normal and Hard files that do the same;
• arl101cr_undead.utc — delete this;
  

It's advised to play Origins or even Lothering without autoscale_FCR_*.gda. If you're going to have only one mage in your party, you don't really need this file. Don't use it if you aren't prepared for a much more challenging experience. I did beat the game with the "Very Hard" autoscale and it took absolutely everything I had at my disposal. Having experienced that, I can't recommend using anything over "Normal" autoscale from the start. You can always upgrade the autoscale difficulty if you feel the game is getting too easy.
1.2 (Optional) Keep "3. HP decrease". Everyone will have much less HP. Results aren't entirely predictable. You won't get your HP back if you uninstall, but new enemies will. I don't recommend this;
1.3 (Recommended) Keep "4. Potion cooldown" folder. Every potion size will be on an individual 30 second cooldown;
1.4 (Optional) Keep "5. Steal cooldown" for 1 sec steal cooldown. Dain's Fixes already include a tweak to reduce it to 0.5 sec;

2. (Recommended) If you want FCR-like ranks in Awakening and other campaign type DLCs, download Improved Atmosphere compatibility files (second download). Move "1. Ranks Updated" to "zFCR" folder, then delete "\1. Ranks Updated\Origins\ARE" folder (important). The rank assignment there isn't perfect, but it'll do. I don't know how to edit DLC files myself;

3. Download the main package from this mod page. Extract and move it into the "zFCR" folder with overwrites;

4. Install Qwinn's Ultimate DAO Fixpack and its hotfix. Install the .dazip using DAO modmanager or an alternative;

5. Done.

Uninstallation: delete the FCR folder. All the areas you've been to will keep all FCR changes.

I find it curious that a lot of areas in the game already have the same rank values as FCR. Vanilla Dalish origin is most notable, all the darkspawn in it are already "hard" and "elite" by FCR naming. Korkari Wilds and most of Tower of Ishal too. Without FCR's optional difficulty files they're basically the same. FCR is not a difficulty mod at its core.

Recommended mods:
Dragon Age Redesigned for much better NPC faces. Tucked Hair mod can be found here if you need it for some of the face morphs.
Dain's Fixes for combat bugfixes and tweaks. Read the description carefully.
Enemy Pull Exploit Fix (v1 is the best) prevents you from pulling enemies one by one with a ranged weapon. With this they'll (usually) pull the rest of the group with them.
Two Specializations Sten gives the Sten his well deserved level 7 specialization point.
Advanced Tactics or Even More Advanced Tactics to improve the tactics options, but I don't recommend increasing the number of tactics slots with any mods, because they make the game easier. You could program your party to handle Flash's Very Hard autoscale better than you do, if you put some time into it. The 6 extra slots from Combat Tactics skill tree are just enough.
Resized Shale makes Shale as high as the Sten.
Theta HD to replace a handful of the blurriest textures.
Battle Animations (male animation set) to make combat walk animations less lame.
"party_barks.dlg" from the main Improved Atmosphere download (Companions\4.1 Dialog Changes\Global Dialog Changes) makes all followers give their location based barks, instead of just one. Only use this one file from it.
"_terra_campfire_fix" folder from MRP fixes missing campfire textures. Only use this one folder.
Ghost Elves, Uncapped Elemental Damage Bonus, Law and Order Fixes, Baroness Reward Fix, Silverite Mines Bugfix, Blackblade Armor Dragon Drop Fix, Endgame Cutscene Fixes, Joining Ritual fix for Awakening Companions, Awakening Runes Fixes.

Tips:
All item DLCs and Return to Ostagar are just dumps of free powerful equipment. Consider turning them off.
Arcane Warriors completely break the game by stacking armour.
Getting Regeneration spell and having it on the tank (with Taunt) 100% of the time is first priority if you're going to use the "autoscale_FCR_*.gda" file.
Best area order by difficulty and level caps is Redcliffe/Circle -> Brecilian/Denerim -> Orzammar/Haven.
Bombs are quite powerful. Buy them or craft them and you will be able to solve any problem by throwing money at it. Something to keep in mind if you plan to use the enemy stat rebalance file ("autoscale").