No inventory shuffle - easy switching between dual wielding, shields, bows, etc.
Balance the Clone spells. Mislead is powerful, Simulacrum is unstoppable and Project Image is... well...
Ba-roken!
SoA is swarming with powerful Undead - Liches, Vampires, etc. As such, Pro-Undead scrolls should be as rare as Pro-Magic scrolls, and items like MoD+2 and Daystar should be
waaay harder to obtain.
Dual wielding is too powerful, thanks to the sheer number of weapons with Equipped Abilities. Either force heavier penalties on dual wielding, or really decrease the number of the aforementioned items.
Melee owns BG2. Sorry. Although i love Magic so much better, and i'm one of those who are sure that "a well prepared Mage can take on
anything",

BioWare seemed to decide that each above-Goblin-level monster should have 75% MR and 3 save vs. spells, with no justification whatsoever. This is just plain stupid. Either you follow the D&D rules about MR and Saves, or you tone down all the uber items which makes melee so good.
Use a different engine. The Infinity Engine is weak.
As a result, ...
... Use a different scripting language. BAF/BCS is weak.