I'm with you on that one. I finally got my Ancestry tree cleaned up (though I still find people with duplicated sources/facts now and then), and unlinked my FTM tree so that I wouldn't accidentally sync it and screw it up again. It's a shame that I now have to update both trees every time I change something, but I figure the extra steps are better than having to go through that whole cleaning mess again!
I'm also leery of using the iPad app, because I think it has caused some duplication issues as well. Which is a shame because it's a pretty nifty app.