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Disadvantages are weaker shields, weak ground troops, and no fighters what-so-ever (probably because you can't put a warp core on a ship the size of an x-wing ). Can't speak for B5, as I know nothing about it.
Actually, trek does have fighters, they are shielded, they do go FTL, and they don't have full size M/ARCs.
Shuttlecraft are light fighters.
Just look at the dominion war (DS9).
There, they have the runabouts with torpedo launchers (medium fighter)
And the military designed-to-be-a-fighter fighters. (large fighter)
You don't actually need a Matter/Antimatter reactor (aka warpcore) to run warp drive, but it requires less fuel and is more compact (size:energy output) than the comparable Fusion reactors. Most ships don't carry enough fusion reactors to move at a decent warpspeed.
Shuttles only go warp 2 or so since they have smaller powerplants.
IMO, Trek vs Wars fighters would suffer worse than the capital ships.
Wars fighters are somewhat stronger than Trek fighters, and the Trek fighters can't use FTL attacks effectively on moving targets.
(I believe that the only chance Trek ships have against Wars capital ships would be "Warp Strafing", where they launch torpedoes at FTL speeds, and the enemy can't see them until they've gone past)