The biggest argument in their favor is that they provide a warm, dry, secure, self contained space - more or less. If it's cold, turn on the heater. If the weather is crappy, go inside & close the door - you can still stand up, move around a bit, stretch, cook, sit, lay down, what ever you want. Don't discount that standing up thing - we did the roof top tent, & it sucked in crappy weather because all you could do was lay down after carefully shedding your muddy shoes (& possibly other muddy clothes) in an effort to keep your bed clean(ish). A camper makes that much easier since you can step inside onto a towel or door mat, shed the muddy clothes, then step off into a clean area. A secondary benefit is that you can store your camping gear in the camper even while it's at home, freeing up garage or shed space.
For me, there are two big downsides: Loading/unloading time, & the physical size/weight. I store my FWC in the back yard. It takes me about an hour to clear out access to it, load it, tie it down, and put everything back (trash cans, cribbing, etc). Then you still have to load your food, water, gear, etc., so add another hour or three (depending on how well you have planned ahead), and you quickly run into a full 1/2 day just getting ready to leave. We don't take any spur of the moment trips with the camper - just too big of a PIA for a quick overnighter. The other issue is the physical size. It's big - wide, tall, & heavy. Between the camper, truck, food/water/gear, we're in the 9,000 pound range. That's a lot of weight when the trails get tough. As a result, we don't always take that interesting looking fork in the road. For us, that wasn't a deal breaker since we were drifting away from the more difficult trails & towards easier points where we would set off on foot/bicycle/motorcycle, but it may be a bit of an issue for someone else.
Adding an annex or changing room to a RTT would give it many of the benefits of the pop up camper, but it still has considerable set up time - which could be a pain if the weather is poor. The FWC takes about 15 seconds to unlatch the top, then step inside to do the rest, where you're out of the elements. The Flip-pac or Habitat offers similar advantages to the camper, but lacks the amenities (built in water tank, stove, 'fridge, etc), but if you're primarily an "outdoor" camper, & only need occasional respite from the elements & a nice place to sleep, they make a compelling argument.