I used to play FFG's game of thrones card game back when it was 'collectable'
One thing FFG made clear in the first installments of the game is they didn't want a game where common cards were crap and rare cards were always ultrapowerful. They purposely made some very good common cards in every set. They tried to make each rare card good and a couple every set VERY GOOD, but were very careful to not make them overpowered.
I think FFG may be taking this same stance with named pilots, designing a game and units within the game so there is no compelling reason to take named versions all the time.
And also remember, if FFG knows that pilot ability X + add-on card A + add-on card B is VERY POWERFUL, they are going to put a point cost on that pilot based on his "highest and best use" (to steal a real estate term)
I suspect that someone drawn to taking named versions of ships just because they are named versions may be handicapping themselves, especially if the aren't putting that pilot in his or her highest and best use.
Maybe try the game using at most 1 named character and filling the rest of the ranks with the bottom tier or 2nd tier pilot skill versions of ships.