Question is, is passive perception only modofied by wisdom or is it by the skill as well, hence passive perception would be 12...?
Passive perception includes proficiency bonus if it has it, so a creature with WIS 10, Perception +2 would have passive Perception 12.
Not entirely sure I'd bother with giving it
Skills as 5E seems really stingy with them.
What's an equivalent Monster Manual creature to a Giant Fly? A bird? One of the Giant Arthropods? Guess the Giant Wasp is the closest, and it doesn't have any skill proficiencies at all.
There are plenty of critters with a single Skill though, usually Perception, and quite a few of them are flyers like the Hawk or Giant Vulture, so I guess I'm OK with Perception +2 if you want it.
Oh, and just to remind you, making
Duck 'n Dive a Reaction means it can only dodge ONE melee blow every six seconds, as creatures only get one Reaction per round.
If you want it to dodge multiple melee attacks per round it'd need to be a trait.
That said, I'm fine making it a Reaction that it can only use once per round.
Also not sure about it only being triggered by an actual melee attack. Real world flies don't only dodge things that would potentially hit them, they jump away from
anything they see approaching them (like a fly swat or bird), they don't wait until it's within melee range. The reflex is probably "hardwired" into their tiny insect brains.