1) No one is interested in the "Vials of mysterious fluid" you get from the Nashkel mines. You'd think that at least Thalantyr or the fellow at the Sorcerous Sunderies would be interested in it's alchemey.
2) The cheesey way the party gets to "help" the children in the game. It seems that so long as the party notes something sad in it journal they don't have to do anything to help. eg) The kid who's somewhat "crazy" from watching his family animated as undead by that insane cleric Bassilus. Or the girl in Baldur's Gate city that asks you to get the ring to rescue her cat. "Here's the ring, now you have your kitty. Go enjoy a homeless existance. We have tonnes of money but won't even give you any since I'm gonig to write in my journal how your life is going to make me sad." I know it's kinda sucky, but if YOU found a kid in trouble (with a good alignment at least) would you just walk away? Take the kid to a temple for cryin' out loud.
3) You can only get 1 set of ankheg armour made at the Taerum smithy. And if you don't choose it right away, you lose the option for later.
4) Otiluke's Sphere problem. (You've already addressed it.) It's the number 1 BG1 "Save the NPC before they die." spell.
5) The ArchDruid in the Cloakwood forest is a pussy.
6) Bears too easily get hostile. They need a longer timer before going after the party, or a chance to leave instead of attacking. Most bears in RL will "depart" when they hear someone coming unless protecting cubs/a kill. Since the party is covered in jingly metal bits, you'd think that the bear might be forewarned.
7) Delainly (The werewolf wench) should have the option to join the party. I know about the other mod, but we need some kind of BG1 version.
The Gullykin store blows. There should be some interesting or at least halfing oriented items in the inventory.
9) Another option for discovering about the whole Flaming Fist take-over, etc... It'd be cool if one could go to a temple to summon the ghost of Scar to ask a few questions.
10) You should be able to continue the game after killing Sarevok and do the TotSC quests at that point. If not, then there should be some kind of delay for chapter 6/7 where "Sarevok is out of touch for a couple months. Go find something else to do until he returns so you can settle this crap."
11) Who made the zombies in that northern farm? It shouts either "mini-quest" or a rumor or something.
12) There should be the option of some kind of "wrath" dialog for Shandalar. As it is now, if you do the quest and are pissed, he leaves before you can extract satisfaction.
Just a few things that popped into me head.