No mod that I know of can combat the abhorrent navigation system, but then again, I've given up on the game some time ago and have never visited the forums ever since. I bet it'll take one hell of a mod to work around the mapping, though.

The story having no focus -- there's a lot of freedom, and the main storyline gets lost in the sea of hundreds of other quests really quick. The Tribunal expansion pack, I heard, improves the journal, but I haven't bought it (nor do I intend to buy it -- yet).

I can't stand Arcanum's combat, nor can I stand Fallout's. I hate turn-based. Give me real-time with a pause button any time, thank you very much.