Six Flags parks seem to like slapping a DC Comics character on a roller coaster and call that "theming." The coaster is still front and center, not the cohesive theme or the overall experience of the attraction. It's the same thing I disliked about IoA enough that we didn't even go to the park the first time I went as an adult in 2007 (I regret that now as I would like to have seen it pre-Potterland). It's the same aesthetic that I hate about Rip Ride Rockit, and frankly, I was so underwhelmed by that ride that I will probably never ride it again. There's no story, no adventure. Just "stand in this queue line, strap in to this roller coaster, and hold on!" Ditto for California Screamin' in Anaheim, albeit with a much better roller coaster. *Please understand, I LOVE roller coasters, but Disney and Universal have consistently raised the bar for themed experiences.
By contrast, consider the Revenge of the Mummy. Theming throughout, especially the "brain burn" scene. It actually took me by surprise on my first ride. It takes a pretty unremarkable roller coaster and elevates it to a much more exciting experience. Space Mountain, Rock N Roller Coaster, et al have a story that's set up throughout the area around the attraction, through the queue line, and continues through the attraction itself. For crying out loud, people are throwing a fit about the Tower of Terror in DCA closing, and it's nothing more than a drop tower! A drop tower with top shelf theming.
The appeal of Potterland, to me, is extending that theming to an entire section of park. A consistent and pervasive theme can be really effective (Silver Dollar City in Branson is a great example of this), and while the traffic flow is definitely an issue, Hogsmeade and Diagon Alley provide a unique chance to really immerse yourself in that theme. The Potter rides could never live up to their hype (I was particularly underwhelmed by Escape From Gringott's - a bad roller coaster mixed with a watered down version of Spider-Man), but the theming means that the rides don't have to stand alone. It's my favorite aspect of Animal Kingdom or Epcot's World Showcase- the feeling of actually being transported to another place. Disney is continuing the trend, with fully immersive Avatar, Star Wars, and Toy Story lands in the works. I do agree with you that the storage situation could be avoided, but they'd have to be more creative than plastic bins in order to maintain the theme.
I get what you're saying, I always thought that the juxtaposition of rides in Potterland at USO was slightly off, with Gringotts and FJ, you have rides themed to every tiny detail, with every aspect, ride cars etc. included, becoming a part of the story, then next to that you have two giant B&M's, where the theming ends as you leave the station, and just becomes a standard inverted coaster. For an area with so much focus on total immersion, it seems odd to have rides which are just 'rides' as opposed to 'experiences' (obviously the fact DD was there already is a major factor here..)
Disney parks with occasional exceptions create these total 'experiences', never wanting anything to seem like a ride or a coaster but rather an immersive 'adventure'. Coaster track is generally themed to minetrains and the like and things like ride cars and 3D glasses are usually included in the story.
So yeah I get what you're saying, and it does kinda seem odd to have a load of Coaster track when you are supposed to be inside Jurassic Park or whatever, but I guess if its a good coaster then does it really matter? I suppose it just comes down to levels of theming and immersiveness which as US parks seems to be sometimes quite inconsistent compared to Disney. It also comes down to personal preference, I am massively into themeing and 'experiences' whereas I know a lot of people dont really care and would rather ride a great coaster.