The primary reason for Mandalay over Yangon was for the shorter bus trip to Bagan, but since you're only flying to save time, my reason for this suggestion is no longer valid.

As far as Yangon or Mandalay, I prefer Mandalay slightly over Yangon (granted, I was only in each city for 1 day ). I felt that Yangon was too busy (traffic jams everywhere due to bad urban planning; they probably didn't foresee having as many cars on the roads as they have now) whereas Mandalay was more laid back and you could walk around everywhere pretty easily (stayed just south of the Mandalay Palace and besides taking a taxi to the U Bein Bridge and the airport, I just walked from place to place). Also, there were more streetlights in Mandalay, from what I remember, so I wasn't in fear for my life when crossing a street at night; the same can't be said for Yangon.