Most of "charges" against BGT aren't really that solid.
EXP gained - BGT limits exp for locks, traps and spells significantly. You are able to switch it off totally (for the whole game of course)
BG1 part limit - you know there is something called "hardcoded exp cap"? In BG1 essentially it was some 161000 iirc, you could've remove it with .exe modification. Now BG2 had it too. IIRC 2950000 exp limit. But since ToB there isn't one - you can go all to level 40 (which is not hardcoded) or with TDD/EoU etc up to 50. There's no hardcoded limit and no way to implement it selectively to BG1 part. If you think that spoils all the fun from beating Sarevok there's a mod that would make them "a little harder" ;)
Ammo stack - nope. BGT uses BG2 behavior "out of the box". In BG1 part shop stacks are still 20 rounds but once in equipment they indeed stack up to 40. Any behavior other than that is no standard (so I guess you switched some option to make it "bg1 ammo stacking". It WILL go all game along! There is no way to switch it selectively in BG1 part. And IMHO there is no point in making so! The whole point of the mod is to make all those changes BG2 brought to us available in BG1 and provide continuity between those two. It is done.
There are 2 wolfweres/werewolfs you can only harm with silver weapons.
I believe "silver" is one way, +2 or +3 enchantment the other. Remember some weapons +1,+4 vs X in reality are +4 enchanted! There's no "selective" enchantment, only hit/dmg bonus so enchantment in many of those is calculated as highest to hit bonus. You can then use bastard sword Kondar you can get really early - it has +3 enchantment. There's also Xan's moonblade (also +3 but only usable by Xan who is PITA). Kiel's morningstar (+3 also), cursed two handed sword of berserking (yes, +3), flame tongue long sword in DT is +4, short sword of backstabbing from Slythe is +3 weapon, balduran sword is +2 but cold iron/silver enchantment so effective against greater werewolves.
All of that I wrote based on RINGLOUP.ITM properties which makes user invulnerable to any weapon with enchantment +2 or lower.
A greater wolfwere increases his healing rate every time you reload, and I had to reload a lot. Finally I had to kill them via console.
Didn't observe increasing healing rate each reload but... greater wolfwere (and probably werewolf too) has incredible healing rate, I remember meeting 3 of them for first time in windspear hills (bg2) resulted sudden death of all my party with "slightly injured" wolfweres after A LOT of punishment by a kensai charname, minsc, jaheira, yoshi&traps, nalia and anomen).
- In the highest level of durlags tower is a succubus. In vanilla I got a quest from her if I approach her with a female char. In BGT I had to fight her.
Nope. The quest goes on... maybe you didn't speak to that thief level lower so there was no option to "kick in" in dialogue.
When changing from BG1 to BG2 the reputation number has been reset, but not the chars. So Minsc was happy and Jaheira complained as soon as I got them out of their cages.
Normal behavior. You either start out with what u left in BG1 (no reset) so after joining all options kick in like if you did plenty of good/bad deeds in a very short period of time (so mild annoying Jaheira with 13-15 rep and heavily annoying afterwards) or you start out with typical rep for your class and alignment (so for lawful good pal it's some 13 iirc, chaotic evil dwarven berserker probably 9 or 8) that already makes some annoying comments by NPCs after joining.
In Irenicus Dungeon you can find items you got from BG1.
Again - you probably switched some "additional item transition" option. After "core bgt" is installed there's regular BG2 behavior - so only helmet and horn of kazgaroth (or some other items, can't remember atm which CAN transit to BG2 but really not all that much you wrote in your post).
- BGT removed the "respawn bug"
Believe me they fought with it a LOOOONG time and I think it's still present if you choose "bg1 style spawns".
BGT makes the game much easier
Well if you feel that way try reduced to 70% exp (there's 30% option too iirc) and maybe some SCS. Small group of ruffians with one mediocre spellcaster can become a real PITA. I recommend no DSotSC/NTotSC but instead BG1UB and BG1NPC.