This has probably come up before within the devs, but why not make the CCS a capital, a la the Autumn and Marathons, and make the RCS the spammable cruiser.
First, the Covenant are kind of lacking in capital ship variety (though I know the whole thing is kind of a work in progress, especially ability wise) while the UNSC have lots of options. It might be nice to have another one in the mix.
Two, I imagine this is at least partly by design, but the Covenant only have access to the DDS until you reach tier 6, at which point you need to invest some significant resources to build the SC, SD, or CAS. You could make the RCS a pre-requisite for the CCS (although that doesn't make sense chronologically), but perhaps make the CCS a tier 4 ship so the Covenant have some mid-game access to another capital.
Alternatively, the RCS could be the capital and the CCS the pre-req. Aside from the CAS and the SD, which are both late game ships, the Covenant don't have a good front-line, brawly capital ship. Making the CCS (or RCS) into a capital and giving it a handful of good pure dps abilities might help mix things up a bit.
However, I imagine the reason the Covenant don't have early-game access to lots of capitals is balance worries, so I don't know how that would play into this/make a big difference. It might be game breaking if the Covenant got a CCS at tier 3 and the RCS capital at tier 4. I suppose if that's the case, a CCS/RCS capital where it is now, at tier 5, would also mix things up.
It just feels a little bland starting with the DDS and then getting no new caps until tier 6-8, which require heavy investments in research.