I really like that you're asking the bigger question about how we actually want the installation wizard to work, instead of blindly just trying to update dependencies.
Honestly I have never tried to touch the current wizard because I assume that it's inflexible, and in an awkward technology.
Going forward it would be nice if different OpenMRS distributions can leverage the core installation wizard by plugging in additional screens and actions. (I don't know if they'd do this with modules or what.)
This doesn't seem right to me. I would expect that the install/upgrade wizard just runs in a shell environment, and does not have all the API and modules loaded up...