I had a '96 when I bought my '03 new (after they announced it was the last year for the convertibles).
The '03 is MUCH quieter and more comfortable inside, and the 2.0 handled my 29" tires way better then the '96 truck did. There's also slightly more cargo room (I can only speak for the 2-doors). As far as lifting is concerned, pretty much anything you could do to the earlier version can be done for the newer.
There still seems to be a wider variety of aftermarket options for track/kicks, but more has been emerging for track/vits lately as they've gotten older.
As a daily driver, there was no comparison between the '96 and '03, and you'll really appreciate that extra 30+ hp. A lot. Especially if you're upsizing the rubber.