I prefer my 2 door 90% of the time. It's FAR more fun to drive, maneuverable, has better visibility, better fuel economy, performance, etc.
All that being said, married with a kid (another on the way) and 2 80-pound Weimaraners.... The JK will soon be traded for a second JKU.
In a warm weather climate, I might hold onto the 2-door, as use of the back seat with no roof is easier (don't even have to open the doors!), but 4-seasons life is more difficult. Soft windows are fragile in below freezing temps, the passenger seat barely slides forward, and rocker panels pick up mud, slush and worm guts to rub all over your pant legs when leaning in to access the back seat.