Sorry to hear about the trouble you are having with the plugin. For questions regarding WPtouch Pro we ask that you access the Pro forums at http://www.bravenewcode.com/support and our support team will be happy to provide fast and friendly support.
-Latest version of WP-Touch Pro doesn't work on the homepage of my WordPress install, all other pages work, but the home page shows the desktop version (with no link to switch to mobile theme)
This sounds like a cache issue. We have tutorials on configuring WPtouch Pro with various cache plugins in our DOCS area. You can access them once you login with your Pro account.
-Home page (desktop version) ignores my query_posts( array( 'cat' => -12, 'paged' => get_query_var('paged') ) ); statement, and shows posts from cat 12 anyway.
If this issue is in your desktop version, we can't really do much there. If it's in the WPtouch Pro version let us know.
-Support is incredibly bad, I managed to get the email of someone that work at BraveNewCode but their answers weren't helpful at all.
Not sure what e-mail address you sent your message to, I don't recall seeing your questions. However, please login with your Pro account at our support forum for questions regarding WPtouch Pro.
To add insult to injury I just cleared my W3 Cache and the whole mobile site stopped working.
Perhaps not configuring the cache plugin was the cause of some of the issues you were seeing. Here's a direct link to the Compatibility section of our documentation - http://www.bravenewcode.com/docs/wptouch-pro/compatibility/