Hmmm.... what would I like different....
For starters, I'll agree on a better variety of weapons. Anything but a sword and couple of staves were sold immediately.
A better quest log for sure. One that indicates quest, task remaining, and where to go back to. 3DO did a good job with this in MM9 -- the quest log updates as you complete steps and tells you where to go next.
Fewer guild quests, or a better way of handling them. It really gets frustrating running around from town to town because Grumpy just made Paladin, so now you have to go all the way back to Valeia for guild levels.
A town portal spell, or something similar, that would let you go to a specific town. Eliminates a lot of the frustrating travel.
Dungeons that respawn (and appropriately!). For example, don't you think that after a couple of weeks, something would decide to move into the crypt? By appropriately, I mean appropriate for your level. At low levels, it might be more skeletons and such. At high levels, it may become the new salad bar in town... imagine the fun! And levels should be calculated as real levels, not actual levels. If I've got to level ten in five classes, I'm not level ten right now; I'm more like level 50. I should get something appropriate.
A final score mechanism of some sort. I really like this about the MM series -- you get a number that tells you how you did, and you can then compete with yourself and others. Adds for more interesting replay, too -- what's the highest score you can get, highest with one character, etc.
Easter eggs. Hidden things that you can use to your benefit (or detriment).
Keep the price on blessed dragon arrows
Your behavior changes the game. Kill innocents, and people mistrust you, charge you more, and perhaps won't give quests until you complete a prequest. Or perhaps you have to prove your worth for one character by damaging your rep with another. IOW, your behavior affects the outcome.
That's it for a quick run off the top.