Reading through the OP (which is very well written IMO) I had more feedback. I really enjoy these discussions.

Systematic Flaws
1. Initiative
Systematic is the right word here. It doesn't feel terrible, and personally I'm ok with it. I don't really have a dog in this fight. As Stabbey said, /shrug, but it makes Wits worthless. Then again, in EE, wits just felt like a stat tax to ensure all my guys weren't going dead last. So I'm not sure I liked that any more. It wasn't fun or interesting to invest in Wits.

2. Armor System
Agree, I provided similar feedback in EE. Everyone seems to have an opinion on how to fix it, but my only feedback is I agree it needs something.

3. Scaling
This is turning into the biggest one. Farming merchants is just tedious. I was so excited when I got Lohar's hammer in act 2, and sold it less than an hour later. One level made it so weak frown I haven't felt excited about loot since. It's all so ... temporary.

4. Random Loot Generation
The nonsensical part has always bothered me, but games like D3/Torchlight/Borderlands have taught me this is a lost cause. Whatever developers see in it, it's beyond my understanding.

5. Character Building
I mentioned this in my review also, but it feels like your first points are so interesting and fun and crucial. After that, you just kind of invest in the same thing for the rest of the game (Civil Abilities), or with tiny, tiny variances to grab must-haves (2 Aerothurge for instance). Otherwise, leveling up is more of a mental groan where I go re-farm merchants.

6. UI
I don't think anyone would argue the auto-adding is a PITA and unwanted.

7. The Ap System.
I disagree the AP system is painfully restricted. I feel like the flow is much better captured now in terms of weak-moderate cost abilities. I can watch the enemy make its moves and mentally tally the AP they've used or saved so far. And going back to DOS1, I was struck at how clunky the AP costs lined up in terms of planning out my turns. All in all, I feel like the AP system is a big step forward in their design. If I had one complaint, it's that the 3 point abilities just don't feel worthwhile (outside of Elemental Affinity to use them), or that some abilities just don't feel useful, but that's a whole other discussion. In terms of AP system, I like that it's fixed and I'm not always out hunting for the king of all resources - AP. It's as static as a turn in Chess or X-COM, and the enemy faces the same restraints.

Conversely, letting me up my AP presents new encounter challenges. Either they scale enemies to likewise get more AP in their own ways, thus making my AP a wash, and punishing casual players who don't min/max for the stat. Or, they leave the enemy AP the same, and trivialize the play for me (see DOS1). It's a coldwar resource and leaving it static is smart design, IMO.

Major Flaws
1. AI is riddled with issue.
Not sure I can fully agree with "The AI is riddled with issues." In EE, the problem was the exact opposite. Opportunist, Shackles of Pain, and using terrain to trap enemies was pointless. They were Neo-In-Matrix in their counterplay. Now I will agree that sometimes it feels absurd (they legit will kill themselves, ruining any step 2 to their plan), but those instances are rare enough where I feel the AI is at least in a better place (i.e. willing to punish their shackled comrade if they have more HP than me). To call it a major flaw feels like an exaggeration. It could be improved. It doesn't feel major, so it distracts from some of your better points.

2. Source as a mechanic
Mostly agree. If it just recharged itself after a fight, I wouldn't care. Making me go farm corpses is ... tedious. From an RPG standpoint, I agree it feels cool though.

3. Combat Skill/Ability balance
Again, some abilities can be improved, but this doesn't feel major. You started out pretty level in your writing, and have slid into a kind of hyperbole at this point. "absolute joke" seems a bit much. Some can be built around, some need re-balancing, and some feel good as a benchmark. That's pretty solid. I'm sure they're aware enough of it (considering their patching so far) that this doesn't need to be stressed under "major flaws" and "absolute joke." More like "could use tuning" and "some feel underwhelming."

4. Tactician Mode
I can't really say, I've only played TM outside of EE. I'm told it's just a lot more HPs, with I'm ok with. The AI seems smart, and not being able to always insta-gib an opponent feels like a tactical challenge to me, i.e. tactician mode. If I had complaints here, it would be that DOS2 suffers from what most TBS games suffer from in their later acts. Act 1 felt ok, but by late act 2, I feel like I can curb stomp anything in non-boss fights. It reminds me a lot of X-COM in that if you survive the early parts, you win. I don't have a useful solution to provide, but that's my feedback on it.

5. Aesthetic Control
I was about to write "major issue?" again, but I can see how some people might consider this big. I'll say it doesn't matter as much to me, but that it almost ties back to the gear grind issue you mentioned earlier. Even if I found/made a slick set-up, it'd be farmed out in an hour or so.

Hmm I shoudl actually do work at work. That's my feedback so far though smile Nice write-up, and thanks for taking the time to put it together and get a discussion going on it.