Will depend on how people want to play. Comp lists are not going to be pretty. But then again how often in a comp has Han fought Han, Vader had some Vader on Vader action, pilots use R2D2 who would never have got to etc.
Both are games and will be dodgy if people play them like a game. I have less problem with mercenary/allied lists in A-wing than I do fighting an Imp on Imp game in x-Wing.
I was talking to a mate about this and they said ' at least I'll get to use all the bloody ships' as he referenced the ships in X-Wing sitting in the case that he never used but got for the cards.
Well, the Trek universe is filled with stories of allies-of-convenience, so it's not even that far fetched for it. You're also less likely to have mirror matches or worse: clone matches. I just enjoy the challenge of trying to have a purpose for it. Why is Donatra commanding a Cardassian Galor-class alongside the Enterprise-D? It stretches the canon for me, and the primary reason I pick up these games is because of the universe they're from.