the size is good. i would not want it any bigger.
give it a new engine, better MPG. also have heated mirrors out side, and a tow mirror option like the tundra style tow mirrors. wheel wells are big enough IMO. and like cody said a real off road package with more then just the locker and sheet mettle skids. and on modles even 2wd, extend the rear diff breather, if not on the 2wd do all the 4wd, they do the front diff but not the rear.
the bed size is good and i have the SB,i like the bed rail system for towing stuff down. i would like some real tie downs in the front like they have in the rear.
thats about all i can think of. i think the 2nd gen is really great as it is right now. and like whipper said, you want/need more space and bigger bed get a full size, it is a mid size truck. also a lot of the little stuff like heated mirrors are all ready on the tundra, and other full size trucks. dual climate control is on them as well.