I agree with pretty much all the suggestions on here, but how about some pretty simple basic stuff that any vehicle in this price range should have...
-a locking glove box
-locking center console
-a stereo system (I know they say it comes with one, but I can barley hear it!!!)
-the 2.7L 4 banger that they use in the Highlander (it puts out about 24 more HP)
-The new V6 in the 4runner and FJ (why do those models get it and Tacomas don't?)
I still would but a Tacoma over any other compact-midsize truck