I'm all for another type of ship, bigger and better then before or no. I don't think we really need a new stronger class- I find that stronger/more expensive variations of similar things grow stale after the 3rd or 4th installment, as a general rule. (I'm looking at you, Advance Wars, Duel Strike)
Having a bigger capital ship I have to say I like the sound of as long as it's not just a capital ship with more stats. Maybe something more along the lines of a mobile Starbase(as an off topic note, I think there should be more then one per civilization). I'd say if it's pretty much a super capital ship, at least make it hard to get or a really limited number. I never liked it when towards the end fleets become saturated with the very strongest units.
If it were up to me right now, I'd say make it HUGE, but only allow one.