Hi Bodhisattwa,
regarding your first proposal,
I'm not sure to understand the advantages of having hundreds thousands books in Commons, right now.
Commons manages metadata poorly, Internet Archive is much more efficient.
I do find that the added value is when the book is in WIkisource, but this means that we need people doing that, human curation. So I find IA upload tool perfect in this regard: it helps you do it when you want to do it, quickly.
For the second bot, I think the problem is simply that every wikisource is different, and creating good index pages is more art than science. Moreover, there is the problem I said before.