The one big problem they face is: how do you organize them? Alphabetically? (Probably too confusing, it'd be too much like an index). The way I'd do it is a hub interface, where you can see the new releases by clicking a button, (with the new hero's icon so you know who's come out), and then once they're old news they get sorted into their various teams. Inside the team "folders", repaints would be stacked into separate hero "folders".
When you design video-games, (yes, I do know a bit about this), one of your goals is an easy user interface. With this method, you would only have three folders to open at most: Team/Hero/Repaint. It's simple and would work better then scrolling through SHSO's many heroes. Just to be clear, I love that they have a lot of heroes, and that they've actually included more obscure heroes such as Morbius, (bet Dazzler's next!), but unless they come up with a good system for organizing the shop, it's going to be harder and harder to browse, and they'll keep archiving heroes temporarily and then flashing them back at us for brief periods of time. My guess is that they're doing this to distract us while they work on a great new system of organization, so let's keep our fingers crossed for the folks at Gazillion!