First of all, I've had both and employed each of them in a variety of settings from Washinton state with brief camping trips into the Cascades and daily trips to ski at Snoqualmie and Crystal Mountain, to 2,000 mile highway trips on the interstate, to Louisiana's swamps, to a week long trip along Texas's trails bordering the Rio Grande. The bottom line is that no matter how you slice it in a jeep, you'll always be underpowered, you'll never be able to stop as quickly as you like, and there'll never be enough room. Period. So why do we drive jeeps? If you have to ask, you'll never understand.
That being said, there are pros and cons of each. The empty roof rack howled in the wind like a scalded dog. Loaded with any amount of weight, it oscilated at highway speeds and made the center of gravity unpredictable when off road. The rack caught on trees and limbs all the time too. The mounted lights reflected off the snow, dust, or hood, making them virtually unusable while driving. But, they looked so cool! This is why Camel Trophy landrovers had a flat black hood and wires that stretched between the grill guard and the rack, to try to decrease the snaggage. Also, it's a pain to lift stuff that high and then crawl up on the rear tire to strap it all down securely. Also, you can't moniter your load when it's on the roof. Why did the rack work on a 110 defender or a Disco....because they're bigger vehicles, V8 powered, with better suspensions and brakes, etc. But it's light weight, you say, and doesn't affect highway speeds and your ability to speed up interstate hills! Well, it seemed to me that even with 4.10s and the 4L, there was enough wind resistance that it was still depressing getting passed by a geo metro with 6 clowns inside. But at least I wasn't a clown riding in a geo metro....
The trailer is heavey, decreases stopping distance, kills gas milage even further ( a problem if you're trying to minimize dependence on gas stations), and they can be expensive. However, you can now easily remove the jeep's soft top without unloading all your crap (one of the only benefits of a jeep over other off road, expedition equiped type vehicles). You can haul dirt and rocks and cement bags and a refrigerator in a trailer, and can't on a roof rack. It makes a handy platform for cooking, roof top tent, bikes, canoes, etc. You can add a water tank, extra battery. You can leave it for the day without breaking camp. Mine pulls nicely and exactly behind the jeep and uses the exact same wheels and tires, thus necessitating only one spare.
If your goal is long distance on-road travel, get a motorhome, you'll be happier. If your goal is long distance off-road travel, get a unimog. If your goal is short distance off road camping, get a lifted toyota tacoma. If your goal is short distance on-road travel camping get a minivan and pop up trailer. If you want to do short, off road trips in an affordable soft top type vehicle, lift a samuri and drive that. If all you want to do is hit the trailer, get a honda foreman or side-by-side and drive that. BUT....if you want to do it in a jeep, you'll need to make a decision.
Please tell us what you decide or decided and post a photo of your combo in action!