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Soo.... I just watched Episode 6 and 7 of Rebels Season 3

-Iron Squadron has already been touched on, but it looked like the ship was only firing forward? I do not quite remember and I only re-watch episodes after I finish the series.
-Fenn Rau joins the Rebellion... I wonder what ship will be the honorable host of his pilot ability? A Wing, X Wing?
-Phantom 2, a Separatist Craft for the VCX. Probably more aesthetic but it doesn't have a turret and is obviously inferior.
-Separatist Droids were encountered as fully functional, but they lacked any ships except the shuttles. Still not enough substantial meat to suggest Vulture Droids except that maybe other tactical droids had the same idea as the one the party discovers.
-B Wing super laser cannon thing that Hera used, even if it was a prototype and the actual ships were modified because the B Wing couldn't handle such a big gun.
- The Mando-Empire guys had a ship that looked like a giant Protectorate Starfighter.
- Rex flies an A Wing in Episode 7

This is all I got so far.

A case can be made for de-coupling pilots from crafts, and have their PS and pilot abilities be granted to any ship... but then that would become a mess of synergies, and card management on the table...

That'd also be a mess for FFG to hit a "re-do" button and try and explain to people who buy the kits off of a local store and stay home otherwise.

My best guess, like Corran Horn being in the wrong ship, is that they have and will continue to ignore select cases. If a ship needs a buff or a new release includes that ship, they'll revisit for new pilots but only in those cases as I think they have done before.