Well,
SFB does mention that it is based on the Star Trek universe (TOS only). FC also thanks GR for the universe (if my memory is accurate). I have played SFB, I play FC, and I play Starmada. So I to am also looking forward to this game.
The look and feel of FC is pretty accurate for most of The Original series feel. Phasers, torpedoes, and shields of FC have the flavor of TOS.
How warp drive, photon torpedoes, phasers, disruptors, plasma torpedoes, and shields work in FC will have to be done in Starmada terms, but, for the most part, the rules are pretty much already there in the starmada game system.
I think how shields work (in games terms) will take a little modification of the Starmada system on how shields work.
In FC, there are shield boxes for each side. You have those shields up on a side until enough damage has been absorbed by that shield to be dropped. Then there is shield reinforcement, etc.
Starmada FC should have shields that reflect the FC way, right? In my opinion, and it is only that, the shields in the FC/ Starmada universe should have the ability to absorb X number of damage points before the shield is downed. So, unless other special rules apply (half-shields, ignore shields, etc), each arc should be able to absorb an amount of damage up to X, then it is down and offers no protection.