I can't even begin to consider the difficulty of creating a unified SFU/FASA/Trek-canon timeline. That alone is a major achievement!

Your version of the Trek universe has the advantage of incorporating ships from the films, Star Trek: Enterprise, and the TNG-era shows - something which no game setting has ever done before (although I have seen some fan-made versions of the Enterprise-D and E for the FASA system). I bought the FASA game back in the day, again hoping that it was more streamlined than SFB. It was, to an extent, but I found the game mechanics clunky and didn't like a lot of the ships. I think many of FASA's gameplay issues stemmed from the fact that the game originated as the ship-to-ship combat system of the Star Trek Role-Playing Game. There was even a version of it where a group of people could each play a member of the bridge crew, working together to run a ship.

A word about the FASA original ship designs: there were some that I loved, such as the Fed Larson and Loknar classes, and the gorgeous Romulan Winged Defender. I also liked that they addressed the issue of the "Klingon" Bird-of-Prey actually being a Romulan design. Unfortunately, many of the Klingon ships were bloated, misshapen affairs (don't even get me started on the Klingon "one-wing" design), and the Gorn ships were almost Borg-like in their blockiness. The SFU's Fed ships follow a design aesthetic first put forward by the venerable (and fan-beloved) Star Fleet Technical Manual, and the vessels of the other races were logical adaptations of the same. Where no example of a race's ships was available from canonical sources (or the canonical source was unpalatable, as in the case of the Kzinti ship from one of the animated episodes), the SFU designer's choices seem much more inspired, imho - perhaps due to his training as an engineer. Compare the SFU's Gorns to FASA's and you'll see what I mean.

SFC was a great game, from what I hear. I never got to play it because my computer at the time was an Amiga 3000. I have a pdf of the book of ship descriptions, which are essentially taken directly from SFB, although the images of the ships themselves differ from the SFU designs.