Just the regular Heavensward profile. I've been testing the flying version for a few hours now, there's definitely been some odd bugs (it'll talk to an NPC, and then continue to wait there to talk to the NPC it's already talked to, and requires manual input to turn it in). And the flying plugin is a bit buggy and requires a fair bit of manual intervention as well. Other than that, the flying profile has helped a lot to pick up the other quests. I just found it odd that the regular Heavensward profile only checks up to level 56 (maybe 57?) then says i've completed everything except flying. Maybe when I hit 59 there'll be more to find though?
EDIT: Just double checked, it gets to "Checking level 56 quests..." and it says I've done all the ones I'm able to do wihout flying. Is flying required for all the 57, 58, etc quests? The profile is very full as it is, and i'm extremely thankful don't get me wrong, I'm just afraid it isn't progressing because of some quest I have to do manually or something.