Things like no exp,combat kill no spellcasting outside of combat, per encounter stuff, individual recovery, the overly convoluted armor/pen, the preoccupation with balance, the postanago, the muscle wizards, the list goes on and on and absolutely everyone who was following along during development pointed these things out ahead of time.
I will adress the issues you listed one by one.
1. no exp,combat kill
Meh. I'm not bothered. There is arguably too much xp anyway. I'm not too attached to traditional levelling system.
2. no spellcasting outside of combat
A very good change IMO. Hate the buffing routine of 10+ buffs per character per rest. This way you have to consider which buffs are really worth it - and which may save your skin in a given situation. Of course you still use the same old buffs too much, but its a, pardon... balancing issue.
3. per encounter stuff
Yeah, not a fan of this change in PoE2. But it does work decently enough IMO.
4. indvidual recovery
And here I'm proud of our Joshua Sawyer. He was brave to try to push the genre forward and take advantage of the calculating abilities of computers, introducing an actual real time based system - instead of fake turns. Also allowing variable attack rates basing on armor type, modal stances, abilities and weapon speeds, as well as variable pulses of spell/ability effects (most effects pulse every 3 seconds, but beams and walls pulse every 1 second).
Now as we all know, he wasn't entirely successfull. The split second effect duration calculations are a bit ridiculous and the flow of combat is difficult to read and follow due to effects lasting extremly variable time units and expiring in a difficult to control manner. I think he should have normalized spell/ability effects to like 3 second durations after all.
Still, it was progres, moving things forward. I do applaud his efforts.
5. the overly convoluted armor/pen
Yeah, its... not very good. Don't know why more games don't copy systems like Fallout 1 & 2. Or Underrail. Still beats THAC0 in clarity for me
And combat in PoE2 is generally very fun, so it can't be that bad.
6. the preoccupation with balance
So you believe in memes? Noted.
I mean there were some balancing efforts, sometimes dubious, like the item nerfs in early PoE2 patch (some justified, others - not so much). But overall these games are are very far from balanced. In fact, they are lovely unbalanced.
7. the postanago
Meh, they did their best to create a new setting, new factions. Is it all brilliant writing? No. Is it good enough? For me - yes.
8. the muscle wizards
Guess that was a balancing act also. All stats have clear, specific functions - regardless if physical or... spiritual in nature. Such clarity works well for me. Also we went from having 2-3 useful stats (from 6) to 4-5. Again, progress, development. Huge INCLINE in my book!
In my opinion these games are indeed beautiful, if somewhat flawed, gems.