Performance with large number of mod (packages): Seems fine. I've got 450 or so and it's fine. I don't know why MWMM had such a problem with large numbers of mods, but it seems that I have avoided it.
Exes: I'll think about it, but probably not. Exe extractors are relatively rare -- I would suggest unpacking them and then repacking as 7zs. Although other folks have reported that just changing the extension to 7z also works.
Part of the reason that I don't want to support exes is the "Open" command for all archives. The open command for exes would just start the exe, which I don't like.
pyw: I've done that for Bash. The main hassle is rewriting the documentation. Maybe later.
Texture manager: I'm not even going to look! I'm trying to keep visit to Morrowind side fairly brief and just pick some low hanging fruit. However, to have your own mix of textures, all you need is a project directory (i.e. a directory under the Installers directory) with the mix that you like. So if your texture manager can be tweaked to automate that, it will work well with Bain.