Basically I find roof top tents on trailers a good idea.
There are many disadvantages with roof top tents, though.
I'm a very experienced camper and I don't like them as much as other people. Here are the reasons:
1. In the morning everyone has to pee. It's a pain in the rear to climb down, if you really have to go. This is especially true if it is dark! Don't laugh, every experienced camper knows what I'm talking about.
2. The car is rocking back and forth if the people in the tent move (I leave the reason why it's rocking up to your imagination).
3. There are situations (hopefully you will never encounter one) when you will have to leave in a hurry. It takes far more time to get down from the car and into the car then it takes from a ground based tent.
4. For the price of a roof top tent you get the best regular tent there is. Quality ground tents withstand weather conditions far more severe then any roof tent on the market. In a good quality ground based tent you will not get wet.
5. You can leave a ground tent on a camp ground and still use your vehicle. With Roof tents you always have to fold up to use your vehicle. (That's why a roof top tent mounted on a trailer is a better idea)
Roof tents sure look very adventurous and cool, put for hard-core campers, I don't think it is a good choice.
After using one several nights/week over the course of a year, here are my thoughts in response to your "disadvantages"
1. That's what the square nalgene is for. (never drink the square nalgene).
Or just hang out the door that doesn't have the ladder.
If you camp somewhere where dogs are welcome.... you might find that an RTT has the huge advantage of being beyond the marking height of most dogs.
2. If the cars rockin' don't come knockin' ! Seriously, though, ground tents don't hide noise very well either. And the mattress-comfort in the RTT more than makes up for the lack of stealth. You could always guy out the roofrack to some trees if you are really worried about swaying.
3. It doesn't take any time at all to get down from the car if you need to. And unless you pitch your tent right next to the vehicle... any time you spend getting down will be made up for by the fact that you are right by the car. Of course, the corollary to that is -- while you on the rooftop, your truck is much safer than camped somewhere a hundred feet away. When we spent the night in Westwood (Los Angeles) we didn't want to unload all our camping gear and crap... so we just slept in the tent. Didn't get a great sleep that night (traffic, drunk college kids yelling, etc) but at least we were pretty sure nobody was going to break in to the 'cruiser while we were sleeping on top of it. Best part: in the morning some kid walked by with his girl and stopped her to describe (in detail) just how much he liked our cruiser. Its a nice way to wake up, hearing someone admire your handiwork.
4. No argument there. An RTT costs more than a regular tent. Much, much more. But then, they are also a higher-quality shelter. Normal tents make big compromises in order to shave weight. A very expensive camping tent likely employs high-tech stays and materials in an attempt to shave 1/2 pound of weight. An RTT doesn't compromise like that. 1 lb more or less doesn't make a lot of difference to our cruisers.
5. Mobility is another good point. But I've packed my RTT in literally 1 minute (while being attacked by swallow-sized mosquitos in Mexico). But if you move around a lot and want to maintain a base camp, a trailer isn't a bad option. That said.... if you really want to setup a base camp, you could take the RTT off of the truck and put it on a stand on the ground. Maggiolina made some racks that were purpose built for just that. It eliminates some of the height advantages, but retains the super-comfy mattress, insulation from the ground, and overall high-quality construction.
In the end... RTT is better than a ground tent if you don't mind the serious increase in price **for most car campers**. There are certainly situations in which the RTT can't work. But in my not-so-limited car-based travel experience, an RTT is one of the best investments we've ever made on our vehicle and increases camping comfort.
I have come from the line of ULTRA LIGHT camping where we could get everything we needed for a week in about 40-50 pounds. I think with a good Thermarest mattress. (extra wide and extra long) the ground has worked wonders. As for inclimate weather has anybody just thought about a tarp? My thinking is 
