Since it sounds like you want your megacarrier out of combat (the next system or two over?) then it should be a proper carrier. Fuel and munitions, and a large passive to help it detect and flee from threats. Fuel is fuel, munitions is troops. I think you'll want a rather lot of them, even using 1 company per enemy ship (assuming 100% strike success) doesn't leave you much of a body count. You're going to need supporting conventional warships, methinks, with your troops going after the significant ships (probably the larger ones) while the smaller get wrecked.
If possible, I'd outfit your mid-carrier (the fast one) with some box launchers and some long range missiles. If a missile has a tiny passive sensor, it can re-assign a target, and guide itself in to some degree. So you could fire off a volley at, say, 25m km for shorter ranged warheads and maybe 75m km for cruise missiles. Link them all to one fire control to save FC space, and when they strike their target they should destroy it and then retarget any nearby ships, allowing you to do damage to a whole enemy strike force at range. The beauty about box launchers is that they're 15% the size, but only reloaded inside a hangar or orbiting a colony. Since these ships will be hangared, you might take advantage of it for some box launchers. It gives you one solid salvo, and anything left alive will be softened for boarding.
Of course, at this point you're trying to fit a lot of tools onto a small ship, so give and take what you want. You could also have an independent conventional warship with box launchers as extra firepower, and allow it to dock after your troop ship leaves, effectively "hot bunking" your hangar space and utilizing it for box reloads. Either way, I imagine vikings using laser batteries and plasma carronades, just shredding enemy armor as they brutally tear into the hull. None of this "piercing armor and striking engines" bullock. We'll just blast them to sand! Lots of relatively small weapons firing hard and fast!
Hangars open up a lot of very creative options, either way...