This is a pretty good discussion. I'm actually surprised there isn't an overlanding section on here for threads like this.
I guess it's like a few people on here have already said, and it all depends on how much kit you're travelling with, how difficult the terrain is that you're crossing, and how long you're staying in each spot:
- If you have a lot to bring with you (either due to many people are in the same vehicle or how long you're staying out in the wilderness, I'm not really meaning to infer anything about how anyone packs), you may need the trailer for some of your gear anyway. And that's even more likely if you have a 2 door.
- If you're travelling over really tough technical terrain or have to manoeuvre in tight spaces (like the switchbacks already mentioned), the trailer can be a bit less than ideal - though if you have a really good adventure trailer you should be able to pull through a lot that you might not expect until you try. Having everything on a roof rack saves you from worrying about where your trailer is, but having the extra weight up there does raise your centre of gravity a bit, so there is a trade off. Plus, if you have really big tires, a lift kit, roof rack, tent and other gear up there, you could have overhead clearance issues that you didn't anticipate. It all adds up.
- If you're doing a long trip through the wilderness and only staying in each spot overnight, it doesn't make as much difference which you choose. But if you intend to set camp, hit the trails, and return to the same base camp each night, the trailer is a better option since you don't have to pack it up. That said, a good roof top tent takes way less time to pack up than a ground tent, so it's not as bad as you'd think to set up and tear down camp every day.
The other thing about a trailer is, if you have the same tires on it as you have on your Jeep (including a spare for the trailer), you have a bit more redundancy if you need it for a really long trip.
I've actually seen a few people do both - a roof top tent on their vehicle, and another tent mounted on their trailer. It's good if you need extra room for everyone in a full vehicle to sleep, or some of you want space to yourselves (or want the kids to be in their own tent).
Hammock camping sounds really fun, but the big advantage of a roof top tent or trailer is that it keeps you up off the ground and away from animals. Most places this won't be a big deal, but if you're in an area where bears, etc can be a problem it's worth considering.
Personally, I'm leaning more towards getting a roof top tent than a trailer, but a tent or trailer is a lot lower on my list of things for my Jeep than some other upgrades. I'd consider get something like the JK Habitat or J180 if I could afford it, but those are about $10,000! It's a really nice setup though.