Pretty much what CVX said. While a RTT is not always ideal, it depends on how you like to camp.
I have done everything from sleep inside the X, RTT, ground castle(ShiftPod) and I have even slept on the roof rack(xoskel) itself when the RTT was at home. These were solo trips, if my girlfriend comes we always bring the RTT.
If you do a lot of camping where you stay in one spot for days(fishing, hiking, mountain biking), or you are setting up and tearing down camp in a different spot every night(Mojave Rd), a RTT is great.
Setup and teardown of the tent itself is a big plus and your bedding stays in the tent, bigger plus. The annex does add some time(15 mins) and complexity to setup and teardown but if you are doing multi-day in the same place it's worth the hassle to have standing room to be able to change clothes and get out of the weather/sun if needed.
The running into town and having to fold up the RTT is a pro and a con. setup and teardown is easy enough if not using the annex but is a con vs ground tents if you are at a campground and comfortable with leaving your tent and gear at camp.
Campgrounds are another thing, with the RTT you are tied to the parking area of the campsite, not a bad thing most of the time but can be depending on the layout of the campground.
Multi-day trips where you are camping in the same spot but driving during the day is a downside, you have to pack up the RTT and either leave the annex on the ground or pack it up as well.
Gas mileage does take a hit as well having a big square thing on the roof, I think I saw about 2 mpg loss, but we are no prius anyways.
Weight is another consideration, 120lbs on the roof can be felt. The rear suspension will need some help, I weighed my xterra and gave alcan the measurements, they recommended 600lb over, I was a bit skeptical but went for it, best decision ever. The rear is very stable with the RTT and camping gear in the back. Even without the RTT on the roof, and the back empty, the truck handles very nice, not too stiff.
As for the rain aspect, packing away the tent is similar to any ground tent, it should be opened and allowed to air out as soon as possible.