As far as FSCRP versions of campaigns, I'd say it's up to you guys. It's pretty easy to list a version number of a campaign as well. You can even use the text file you create to delete old versions of the mod to replace it with newer ones. If Goober wants, I can writeup a short how-to on the text file from what I've figured out already.
A writeup would be very much appreciated.

In fact, if you're up for it, a wiki article would be ideal.
I should mention though, because it sounds like it may have been unclear -- the "VERSION" token in the mod file is used internally by the installer, not shown to the user. The installer will compare this with the installed version to see whether the mod needs to be updated. If you want to provide
the user with different versions to choose from, then you should explicitly list them. See the
FSO config file for an example.
However, before that I think the installer needs more testing. Some things don't seem to be working 100% and I'm going to spend some time this evening to get more specifics.
That's also much appreciated.

One thing I'm noticing is that every time the installer is run, it leaves an instance of javaw.exe running in the background (which also locks the log files from being deleted on Win7). New instances of the installer can't overwrite the old log file creating lots of log.1, log.2, log.3. Dunno if that's intentional, but it's annoying.
Uh, hm. Nope, that's not intentional. The Installer starts up a bunch of threads whenever it runs, but it's supposed to be shut down when it exits. It sounds like the shutdown may not be happening in your case.
Occasionally, 'Setting up the installer...' seems to run indefinitely.
Is it actually doing anything, according to the log? If the mod config files are taking a long time to download, the initialization might take some time, but it should eventually time out and continue.
EDIT: I'll check the log.
It didn't even try to download any of the sub stuff, like Music, of CBANIs.
Argh. This is probably the same bug that MatthTheGeek ran into, where MVP child VPs wouldn't download. At least that tells me where to look though.