Raven, this is why MediaWiki has extensions— so that you can make it do what you want. (Of course, it would take time, effort, and knowledge of programming in PHP, but that's where the user base comes in.) And once those extensions are written, they're effectively done (at least till the next software update, and then the extensions may or may not need to be tweaked). So yeah, there would be a massive upfront effort to configure/test/beat the wiki into submission, but I don't think the post-implementation upkeep would be as onerous as you think.
About the forum: it would not be an "offsite" forum. The forum would, in fact, be at the same website as the wiki. Hell, it would use the same backend database. Yes, there would be (are) issues with account creation and authentication, but again, see above re: coding extensions. And, at least theoretically, we could get an extension written that would create a forum thread for each page of the wiki (though I have no idea how much effort that would take).
Ratings are in the same boat— it would take a new extension or a modified existing extension to get the particular functionality we'd want from a ratings system, but again again, see above re: coding extensions. And again, once the extension's done, it's effectively done.
phpBB has a built in private messaging system.
The bots would have to be reprogrammed to point to the new site, but again again, once it's done, it's done. And honestly, I have no idea what would have to be updated on connected wikis besides some links, but… have I mentioned that once it's done, it's done?
Now. What would we get assuming the migration is successful? Autonomy, control over the site and its software, not having to depend on Wikidot for new features that may never come. Is that worth all the time and effort and wailing and gnashing of teeth that it would take? In the long run, yeah, I would have to say it would.
[added:] Also, until we have a good feeling that the new site is going to do what we want, nothing will get migrated. Furthermore, even after the migration, nothing will be removed from the current wiki. If Something Bad happens over there, the wiki will still be here.