I've never had a TJ so I can't compare there - but I have had (2) 2 door JKs and a 4 door JK. The 4 door JK is awesome on space compared to the 2 door, especially if you have people in your car other than yourself quite often. The 2 door is the way to go if you don't, just pull the rear seats and it has nearly identical room to the trunk of a 4 door.
The downside to the 4 door (imo ofcourse) is the fact that when you want to go topless or doorless, it's more work, etc. When you just take the top down with no doors off, it doesn't feel very "open" in the front seats.