Well, I showed my design to some others (namely, my mother), who promptly asked why the walls between systems were all different sizes, then called my explanation stupid. So, after being thoroughly annoyed, I redesigned the cabinet.

The top shelf, now with 4 systems, holds an original Game Boy, Game Boy pocket, Game Boy Color, and Game Boy Advance SP, all of which are now standing upright. Every other shelf has been downgraded to two systems to keep the walls the same size. Row 2 holds a DS lite and a 3DS, with an unused middle section. Row 3 just barely manages to fit a 3DS LL and a Game Gear; obviously the Game Gear (and several other systems) will have a large amount of vertical headway, which I may alter and fill in some, or not. As an afterthought, I should mention all DS systems and the SP are displayed opened. Row 4 holds the NGPC and SwanCrystal, again with an unused middle section. And finally, row 5 will hold the Sony handhelds, PSP and Vita, again just barely. Overall, the cabinet now runs 420 mm × 750 mm, or ~1'5"×~2'6". The depth is still the same, 45 mm/~1.8" on the right side, and 55 mm/~2.16" on the left. I also added the glass door this time, and some rather square hinges as I'm not familiar with curved objects yet.
As far as a company making shelving solutions, it's a little harder I think that just doing so. So many collectors, their primary market, have widely varying tastes and aesthetic choices, it'd be very difficult to come up with something universal that a majority would enjoy. Some don't collect for certain systems, or may collect for much lesser known systems; for example, if I was planning on selling these, it'd be disadvantageous to people that have a Game Boy micro, Atari Lynx, and Game & Watch, Game Boy Light, etc. And it'd be very difficult, I'd think, to try to come up with some kind of modular system to ease this, although not really impossible. It just seems a large amount of work for what feels like a small division of customers; sure, there are plenty of people that can and will buy old games, but I'd imagine the collectors and displayers are a much smaller number overall.
As far as making each space identical in dimensions, I certainly see where you're coming from. And this newer design is currently a lot more in line with that, but I'm unsure if I'm keeping it that way. My main concern with that is that the entire purpose of building this for my handhelds is to make something that is explicitly for them, and therefore sized for them. Otherwise, I may as well go down to Lowes or something and buy a simple bookshelf or something. It just seems... proper, for them, in my own opinion.