I am not extremely well versed in EU, and a tad lazy, but who would pilot these ships?

Maarek Stele is it, as far as I know. FFG would have to make up some pilot names.

Having no named pilots only generic squadrons would be an easy way to differentiate them and balance (the missile boat)

My guess to make the missile boat work is to include a mechanic from Attack Wing, where you "disable" a card instead of discarding it. You have to use an action to remove the disable. Include it as a missile boat dependent upgrade or mod called say "ordinance magazine" that give missiles or torps the disable ability and a dial in the defender or advanced range should let you model a missile boat relatively accurately.