If it's going to be your daily driver with the family, then the 4-door would definitely be more comfortable.
As far as offroad capability, the 2-door would be able to squeeze through tight passeges better, but I've seen several cases where the longer wheelbase of the 4-door made it easier to climb over things.
If you ever plan on towing anything behind your Jeep, the 4-door is capable of towing a heavier load, due to its longer wheelbase.
And personally, while I think a stock 2-door looks better than a stock 4-door, I think a built up 4-door looks better than a built up 2-door. And although a 4-door would require a higher lift and/or bigger tires to achieve the same breakover angle as a 2-door, that just makes the 4-door look even better.