Have you considered buffing the Colonial Jupiter Titan? It seems to suffer from a lot of the same issues as the vanilla Ankylon, namely low damage and poor fleet support abilities. For what it costs 2 Mercuries are a much better investment in terms of damage, support, and strikecraft.
EDIT: If/When you get around to racial relationships, the Hypercorps should probably have a bit of a penalty when dealing with the Colonial Loyalists due to resleeving being too close to Cylon resurrection for their liking, and the pro-Zarek Separatists should hate the transhuman ways of the Hypercorps.
EDIT 2: The Mercury is the Colonial Swiss Army Knife: it can tank, it can heal ships, it boosts, mitigation, it has strikecraft, it can bomb, and it can nuke enemy capitals with Medium Yield. I'd nerf the Mercury's HP and buff the Thor's HP to make it the fleet's main tank, and since IIRC the Pegasus had some EW capabilities in the show, I'd give the Mercury-class an AoE debuff of some kind to enemy accuracy to represent some ECM instead of the nukes to give it more of a fleet support role. I'd also nerf the Mercury's armor a little bit too since it has a fair amount.
Oh, and change the Nova's DPS spread a little so it defaults to facing its targets and therefore uses High Yield more often.