@Frederick Ding - I read your proposal, but there is no place to comment there, so it comes here...

You are crossing the line between export and backup. Export is about content not site functionality. In my experience in most cases when you move a big site it involves redesign of the site, so worrying about keeping the old theme/plugins/settings is kind of pointless for those people.
And then there is the possibility of partial content export and import, like if you have an author on your site and at some point he wants to migrate to another site which is not his own. Here he can't force his old look on the new site.

As for the usage of XML-RPC, it is on in 3.5 and you need to use a plugin to turn it off.

In any case I think that migration needs much more love then the importer. If you can add migration options like changing "local" links to the new URL scheme, that will be cool by itself even without fixing the other importer issues.