I didn't really expect BB to win in the Best Actor or BSA categories. Based on the submitted episodes, at least. I think Paul could've won for "Madrigal" but he submitted "Buyout" instead which didn't exactly scream "Emmy"! Cranston was mostly playing egomaniac Walt this season, which while awesome, didn't quite hit the level of holy shit acting we've seen from him before. I'd have probably gone with "Fifty-One" instead too (though "Say My Name" would've been a close runner-up). Mike was a much more subdued character emotionally so while Banks' reaction to being totally vulnerable in that episode was heartbreaking, the competition deserved it more.
That said, I hate to expect anything reasonable from the Emmys, the stars are all aligned for a sweep next year. In addition to it being the farewell season everyone involved has been knocking it out of the park even by this show's standards. Everybody's been turning in arguably their best work of the series i.e. Aaron Paul in "Confessions". But while I'd like to say that Cranston tied his Emmy up with the phone call at the end of "Ozymandias", it's worth noting that these are the same people who didn't give him the win for "Crawl Space" back in season four and his performance in that episode is something that I'm not sure will be topped on that show.