So in BFG:A 2 you select all of you Fleet Setup, Skills and Upgrades before you get matched.
This was different in BFG:A 1, where you got a loading screen, saw your enemy's Faction and then selected a Fleet/Ships
This added another Tactical Layer to the game, you could try to counter the enemy and vice versa.
I really liked the System in BFG:A 1 better.
Especially when you for example Play with some Morale Damage skills and get matched against SM you basicaly choose one or several useless skills/Upgrades.