Random encounter bosses, and/or some static bosses that are incredibly difficult. More things to do in the world (collectibles, gatherables, treasures, etc.) I can list off some things that would be awesome, but don't exist as mods. Also, when looking around at mods, there aren't really any significant ones, only naked-women mods and eye candy ones (more plants! but your computer might melt.). Even the big 'fan made' 'unofficial' big patches actually break things even if they fix others.
They are unprofessional, and can hardly be called QA tested. Most of the time they never get fully finished. 9 times out of 10 they've been left half-finished for 2+ years.