Lifting them is pretty much the same, but I know you can do more fender trimming with a 2 door (only an issue if going bigger than 33" tires I believe).
The shorter wheel base of the 2 door will give you an advantage where tight turning, needing less lift to clear obsticles, and rock crawling. It's lighter, so it should have slightly better gas mileage (2 or 3 MPG?), and a bit more "pep".
The 4 door has significantly more more room, and will be more stable at speed (advantage on trails where you can open up the throttle more). It can also protect the rear passengers in the event of a rollover.
For the kind of camping / wheeling / snowboarding etc I do - I've been happiest with my 4 door as a better "all around" vehicle. It can keep up with 99% of my friends when wheeling - it's only the most extreme of rock crawling / obsticles I shy away from.


Before lift:

After 1.5" OME:

[img width=533 height=400]http://i74.photobucket.com/albums/i246/Jeremiah_Junkins/Tracker/Feb2008snowwheel