Since pilots with offensive skills (Wedge/Backstabber) typically get focus fired down at the beginning of the game while defensive skilled pilots get ignored (Luke/Dark Curse), I think it might be best to gear them with what they are lacking.
Wedge + R2D2
Luke + Marksmanship
This creates a bit of confusion for your opponent when deciding who to focus fire. And it allows flexibility for both fighters to perform well offensively or defensively depending on the situation.
On a related note, it seems inefficient to load up one ship with multiple upgrades (even though some upgrades synergize well like Marksmanship and Torps/Rocks). Mostly because your opponent can largely ignore your other ships and focus the one expensive ship down early to secure an easy win. I've been spreading the upgrades and taking less of them in favor of more rookie ships for this reason.
Anyone else doing this?