The resurrection mechanic, Caruga, is definately a weakness of the BG game. It's mainly because it's so annoying to have handle. There isn't really a problem going to a temple and paying for the resurrect, it's having to make space for all of the equipment and then re-equipping again.
I don't like the idea of experience scaling, it can lead to very skewed gameplay, look no further than Icewindale 2, where you stop getting experience in battles becuase your level is higher than the enemies. It was infuriaitng fighting a battle that required all of your tactical skill and then to get nothing at the end of it.
I do agree that Watcher's Keep needs to be modified. In particular I dont think it should be avaiable at the start of BG2, it's too easy to get in early, clear some of the first level and get +6 items in the process, which naturally imbalances the game. The keep should be available from the start of ToB and from a midpoint in BG2. As for Tales of the Sword Coast, I think the new content was sufficiently difficult in that, that it wasn't particularly easy to gain undue advantage from it early.
As for exploits, I agree. I seem to remember that sometimes enemies chased you if you left the screen, although that may have only been with the Sword Coast strategies mod. The fact enemies do not open doors though is definately something that needs to be improved.
Finally on the topic of minor inconveniences, one arose in particular with bows and shields. It was possible to equip a bow, but not a shield at the same time, which is fine. But more problematically, it wasn't even possible to have it in the slot. However you could pause, take down the bow, then put the shield up with a weapon, meaning you could do in several stages what you couldn't do in one. Let the shield be put in the slot, but only used when using a one handed weapon.