Dude, if you pulled your 4.0 wrangler up beside my 2.5l and you didn't have your junk RIGHT, I'd have smoked your ass like a pack of marlboros. It just depends on what you want to do. The four cylinder costs more money in the long run. You have to build it more, run it harder, and keep your rig as light as possible. The 4.0 is easy, just a couple of mods and you are there.
I would have to say the 4.0 is a better choice all around, but don't be scared of the 2.5l you can have lots of fun with that engine too.