At this point, I'm not concerned about the EU's canon and continuity validity anymore. As far as I'm concerned, if it contradicts the films, than it takes a back seat (Lord knows how many times EU contradicts itself; too many hands in the pot so to speak). Otherwise, it's fine.
Honestly, I really don't see Lucas blowing canon and continuity in they way so many people claim. Yes, there are some canon and continuity problems that need to be explained, but I think the issue stems more from the general dislike of where he took the saga. There are contradictions between the films in the OT after all. lol Thankfully, only a few.
Personally, I rather liked Boba's origin. 3PO's and R2's didn't bother me. And I liked Anakin's as well. I assume Anakin spent many sleepless nights working on 3PO. It was his passion and he was very good at it. lol E.T.'s species was just a cameo and really a non-issue.
Regarding Watto, you gotta remember Qui-gon was a maverick Jedi and it's safe to say that at least the great majority of Jedi would not try to manipulate one's fate as it goes against their code. So I'm certain Watto didn't expect him to do such a thing.
The midichlorians was not the force itself, rather a way to identify it and the potential of the individual. Also, there were certain revelations of the force by the end of the prequel trilogy that actually moves quite nicely into what Yoda and Obi-wan spoke of in the OT.