Yes, fuel cell engines don't require additional shielding and so can easily be lighter than fusion ones. But that and the single free heat sink they get are already the only two advantages they enjoy over internal combustion engines...otherwise they work just the same, and for that you had to get to a tech level/rating that also allows you access to fusion power already.
So while a fuel cell-equipped combat vehicle as allowed by TacOps can potentially carry more armor and weapons than a fusion-powered one, at least as it doesn't try to mount much in the way of energy weapons...the fusion-powered one will present much less of a logistics headache due to needing much less fuel (for game purposes pretty much none at all) and being safer to operate, thus helping preserve trained crews (fuel tank crits may take out the engine, but won't blow up the whole thing -- add CASE to guard against ammo explosions and you're about as safe from crew death via inopportune crits as the rules allow). Given the apparent size of the armies of the Star League, which shaped many of the military traditions of the BT universe, I think I can see why fusion won out.