I'm a long-time lurker but a lover of Bootleg, and I've been waiting in earnest for 0036, because a great friend of mine has never played FF7, and I want to give her a really touched up and remastered version of it to enjoy.
Pit, I think what you should do is release what's working now, get some input, and see how you feel about what's in place right now-- if you just keep adding features and mods and testing, you'll be more and more uncertain of what you're up to with time. Small releases to add little things bit by bit is a stronger method of mod development in the case of a compilation installer (I take my cues from the Big World mod from Baldurs Gate, which does almost exactly what your Bootleg does, but for Baldurs Gate, and with about.. 250+ mods.)
Size isn't a big deal, but you should keep it as low as you can-- and include essentials that you think are really core to improving the game. In my case, this would be retranslation+menu overhauls+high quality avatars+bugfixes (Like the Mdef bugfix/9999 limit breaker) and other things that don't change the actual gameplay or models or anything like that, but update the things that really needed the most work about the game, and that's text layouts, bugfixes, etc.
Bootleg as it is right now is totally fine and not counter-intutive at all. What I would suggest is that you add an automated process for fetching the mods and installing them to the default directory (or a chosen directory). You already have all of the links programmed in, it would not be hard to simply fetch them as well and drop them into the FF7 or mods folder automatically; this would allow people to simply customize the installation in any way they see fit, and for you not to have to worry about releasing mod packs or the size of Bootleg, etc. It'd give all the power to the user and lighten the size of Bootleg down by a lot, or at least prevent it from swelling up.
Just some things to think about. Thanks for Bootleg