I'm a little confused when you mention that Apostrophe has a "lack of module support." Apostrophe does have modules (apostrophe-snippets, apostrophe-blog-2, apostrophe-events...) and these can be extended at project level without modifying the originals.
I think you really mean that you can't package up a bunch of improvements to a bunch of modules in yet another npm module (a "theme") and release it... doing the thing you can do at project level, but in a reusable module.
The ideas you're proposing are pretty much all standard in A2 0.6 (the unstable branch) - but since it's a complete rewrite and we're not done yet, it's not quite ready for prime time yet. Thanks to the moog and moog-require npm modules, the apostrophe npm module contains many Apostrophe "modules" which are core services in just the way you're hoping. You should check out the unstable branch of the apostrophe module and take a good look.