Compared to BFG ships will turn on a dime in FSA (i.e. they turn very quickly). The damage system is different with the FSA system being, dare I say, more random. Targeting in BFG depends on how the target ship is moving relatively to the shooter whereas in FSA it is a function of range alone. BFG is an IGO-UGO and FSA is alternating activations where the players take it in turns move a ship of a squadron at a time.
Just from the top of my head. The feel is quite different when you play I find.
Good summary of differences.
Also, due to the turn structures FA lends itself better to multiplayer than BFG.