I agree a 4 door is more practical however depending on what your actual usage is, it might be a better compromise to keep the 2 door and deal with the issues that come with it and every other Jeep in history versus spending all the extra money to justify a 4 door just because there's more room.
I grew up in the back seat of Jeeps for my whole youth and never complained. From a CJ-7, YJ to a TJ. Then again, there wasn't an option out there
I often wheel with JKU's and in our terrain, the JK's and TJ's have a definite advantage. The 4 door guys work alot harder and I've seen them get hung up and rip off rear fenders. I will take the hassle of loading the kids in the back versus having to negotiate our tight trails with an extended wheelbase.
It all depends on your terrain. I'm sure there are alot of places out west where a JKU is better than a JK.
When I go wheeling, I go to relax and have fun. In our woods, a short stumpy wheelbase is more fun and can fit better between the trees.
I only do day trips and have no problem hauling everything I need. If you plan on going on multi day trips or camping, I can definitely see an advantage with a JKU.
As stated in previous posts, when you sell your Jeep, you can't expect to get your money back for what you invested in it so you might as well use it.
I have seen some pretty cool offroad trailer setups and it might be something to look into for the times when you need to haul alot of gear with the family. Might be a good alternative compared to starting all over again with a JKU