Before I go on, I should make a disclaimer that I've had a few FC-related items published by ADB, but I don't work for that company myself. Is there a particular scale of play you prefer to go with? How much detail do you like to have on your ships, or on those of your opponent? And do you like the concept of duels or smaller squadron encounters more, or less, than larger fleet actions? FC sits somewhere on the spectrum between the individual complexity of Star Fleet Battles and the more fleet-oriented systems like Starmada or A Call to Arms: Star Fleet. An FC Ship Card looks somewhat like an SFB SSD, but there are certain granularities that are changed (or removed) in the conversion from one game system to another. For example, FC forces ships to pay double the amount of power to fly backwards, but allows power generated from any source to be used for any purpose. (SFB ships can fly backwards with no penalty, but can only use power generated from warp or impulse engines to actually move the ship.) Also, shield reinforcement is handled differently in FC, as there are less opportunities to bolster one's defences in this manner here. These changes help put the onus on keeping up a high battle speed to a greater extent than in SFB. To use the Federation Constutution-class CA as an example, the SFB version of the ship is limited by the need to assign power generated by its warp and impulse engines to movement, and to use warp-based power (from the nacelles or from onboard auxiliary warp reactors) to arm photon torpedoes. The FC CA is much more liberal in where its power goes, and has no equivalent restriction on photon arming, but can't go around flying backwards to the same extent and can't decide to go slow and dump a bunch of power into a shield or two either. But if you don't particularly care for the concept of energy allocation, and would rather abstract things to a fleet level, either the Admiralty or Nova editions of Starmada would cover this, as would the upcoming revision to ACtA:SF. (The latter does have a "power drain" concept which somewhat mimics the kind of choices an SFB or FC player would have to make with energy allocation, but does so in a much less intricate way.) There are a number of options out there, but which one (if any) to go for would depend on what kind of setup you'd wish to go with.
If you want to see how the game plays, there is a FREE download of the very basic rules: http://www.starfleetgames.com/fc/FCFirstMissions.pdf
I played SFB for years, but got out of it due to a lack of players - literally no-one wanted to learn how to play the game thinking it was way too complex. Love Federation Commander, as combines SFB with simplicity, so you're able to fight large battles in a relatively short amount of time, but I've got a bit behind with the add-ons, need to get myself some Andros!