I think in the end it is going to come down to the style of camping you're looking for. As you can read from my previous post, I was waffling back and forth until I decided on a popup and I'm glad I did. My popup has been great for going onto backroads while not even noticing a camper is in the bed. It is also great for using my vehicle as an everyday truck for things like taking the boat to the lake and using the truck as I would if the camper was not attached.
I have had my camper for one season and still haven't had the need to use the storage areas around the cabover bed. I have a bathroom and prefer the cassette toilet, it allows me to dump in an outhouse or directly in the sewer access ports at my house without the mess and hassle of what would have to be a very long hose. I have not ever stopped at a dump station, for example.
It is true that come features cannot be used in some popups when the top is down (notably for me would be the bathroom), but I generally avoid using the bathroom in my camper if there is one available elsewhere; the camper bathroom is used in remote locations where I will usually have the top up anyway. Popping the top is an extremely fast and easy affair, so you could always just do that pretty much anywhere in a pinch. If I want to travel incognito, I can still use the dinette bed if I want and be perfectly comfortable.
Finally, if I open all the windows in my popup (see info on the model below), I would have windows all around and those views are hard to beat.
Good luck in your search,
Mike