I'm replaying this as well, still early, just got caed nua, have had it since launch and have a good chunk of hours in it throughout various characters.
I definitely agree with a fair amount of your sentiments when looking back to when I first picked up the game, but now I feel I "get" most of the decisions.
Combat is this weird mix of kitchen sink and rock paper scissors but CC is key in it, especially on POTD where you will run into 12 plus enemies at times.
Lots of kiting, lots of doorways etc. Which can certainly get tiresome.
I remember my last playthrough I dropped right around twin elm/wm2 and same deal with the (ice?) dragon...the one in the cave, because suddenly the game puts you in an arena where position and cc mean fuck all.
I think most of the issue for me revolves around PoTD and the stat increases, especially for dragons. There are powers/spells ciphers and wizards get that can absolutely make the fights with dragons easier though.
The mess with effects never really got to me, I suppose because I played cipher in almost all of my playthroughs and it required me to micro and pay attention a bit more than say a fighter.
At least for me, it helped pick up on the nuances of abilities quickly, when to use, what to use etc.
The per rest system is something I VASTLY prefer over per encounter across the board, I like that there are a mix of them though, and as said earlier, if you get in a fight where you use all of your wizards spells, so be it. I get it's a waste of time to travel back for supplies, but I dunno, I like the idea of having limits on things.
I will say from playing this for almost 100 hours at launch, putting it down, and picking it up for about 10 hours a year or two ago, then picking it up again this past week, some things seem different...
Loot seems worse. I seem to be finding much less equipment and not nearly as good. It seems to be focused on purchasing stuff from the deadfire guy and vendors, at least early on, which sucks for a dopamine hit, but whatever.
Latest patch fucked up some barks and audio too. Overall though I still enjoy the game for what it is and will eventually get around to playing 2 before my kids put me in an old age home.