I'll try to answer this honestly, especially since I too was one of those "emotional" pop-top purchasers.
My favorite thing about my pop-top is that it creates an (albeit small) living space for our family of 3. With the upper bunk stowed, we can stand up, move around a little, play cards out of the rain, and even prepare a light meal (although I refrain from doing any cooking other than warming liquids).
My least favorite thing is that my particular top was 20 years old when I transplanted it from another van, so it's showing its age. I'll need a new tent eventually, and the gelcoat probably could stand some attention.
To address some of your RTT points:
* Yes, expensive compared to a "tent". Pop-tops are expensive compared to even an RTT, which is saying something.
* Interior design is a whole different thing. My pop-top is part of the whole van as a system, not just the sleeping area.
* Yes, you can only camp where you park. As a tradeoff, with a pop-top, your total footprint == the vehicle footprint. Anywhere you can park, you can camp. (Important in some areas, like the desert near me where you are limited to parking/camping where you won't trample native vegetation, etc.)
* Leveling the vehicle helps for sleeping, but you can level after you pop the top. You can pop the top for quick stops, for example, without leveling.
* My pop-top didn't add a whole lot of weight vs. the roof that I cut out, but some. The roof rack and what I put into it makes a bigger impact on how the vehicle drives.
* Peeing in the middle of the night is one reason we went with a pop-top instead of an RTT. We have a porta potti in the van, it slides out of a low cabinet. No opening/closing the van, and the only climbing is for whomever is in the upper bunk - but you can do it in your PJ's without shoes. OTOH, using the loo inside the van with your family requires a strong family bond. Same basic problem with any small camper, though, unless it includes a WC with a door.
* Pop-Top is faster to deploy and stow than an RTT. 20 seconds up, maybe 2 minutes down if I'm taking the time to tuck the tent away from the latches and make sure they're tight.
* Tent dampness is probably the same issue - but I live in SoCal.
My major negative is that its no good for basecaming with trail-runs during the day - you have to close up the top and stow your gear to leave camp. But then again, that's true of every solution except either a trailer or a ground tent...