The only real threats the enemy will have to a flight based opponent will be enemy Saber, because enemy saber is terrifying but it won't be due to anything that he can do weapons wise; and enemy archer because that's their job. The others will have to cheese it. At this point I'll be honest I'm going to have to make enemy archer on a higher tier than I wanted because they'll have the exclusive job of dealing with Perseus whenever he is flying. I'm not even being dramatic he has disengage A on top of his high speed, and his flight how else am I suppose to deal with that? Medusa was so handily dealt in some scenarios with is because Shinji is legitimately awful master who can't properly supply her with mana to make use of her move set because Sakura is her legitimate master. 

Be it as it may that he can exclusively only use one noble phantasm at a time according to the wiki two of them have as stated put the other classes in a hard spot. I'm not even sure if he can use Medusa's head on his own but I'm sure i'd not even allow that because that'd be the equivalent of not only empowering the bag but taking Medusa's Mystic Eyes which is a skill of hers on top of taking her mount.

Regarding the heal factor the enemies won't be brain dead like Spartacus but many of them are close range oriented opponents who are battle nuts.

That's not taking into account our other servants who will also be engaging these enemies at the same time. Lancelot, as poor as his skills actually are, is still a tremendous boon to Black Faction, and Foreigner seems to be settling around by disrupting mana flow.