Great Topic! Thanks for giving us the opportunity to give you some input cricket.
In Starfleet battles (I'm not so familiar with the newer Federation Commander) the speed ships could attain was a complex relation of how much warp power they had and how much they were willing to dedicate to just movement. Trying to port that over to another game would be painful at best. However the extreme cases should probably be considered (e.g frieghters on the low power end and fast cruisers on the high end).
Perhaps though the more pressing issue is maneuverability. SFB (and I believe FC) ships have turn modes. This is generally related to the class of the ship, but varies from race to race. I think this is actually the most important aspect of movement to capture, given that most warships had similar speed limits.
So here's my two proposals:
1) Base thrust on turn mode
This should be quite straight forward since all the SSD's clearly list the turn mode:
Mode Thrust
F 2
E 3
D 4
C 5
B 6
A 7
AA 8
Ships with lots of spare warp power (e.g. fast cruisers or X-ships) should get some bonus thrust. Ships that have less warp power than they need to go "full speed" (e.g. monitors, frieghters, tugs - but not battleships or dreadnoughts) should get a bit of a penalty on thrust.
This would give a Fed CA a thrust of 4 and a Klingon D7 a thrust of 6 - which I think speak well to their relative turning ability.
Any ship listed as "Agile" should probably get overthrusters. I wouldn't want overthrusters to be a really common thing on ships.
2) Add new Ship Traits for Maneuverability
Definitely a more complicated option as it requires coming up with sensible new traits AND finding an appropriate cost for them. If this could be pulled off then I'd have some much different "thrust" suggestions - probably based on the ratio of warp power vs. warp movement cost - which would actually land most of the fighting ships in about the same area - but with some exceptions (e.g. new Romulan "hawk" series ships have lots more power than the original "eagle" series ships).
-Tim