Let's look at the running theme here... this is main games, however. No addons(WC:SO, etc), or extra "free games"(secret ops) should be counted in this... those were, more or less, bonuses that branched off of the main plot.
WC1: Fight the Kilrathi.
WC2: Fight the Kilrathi+Fight Conspiracy.
WC3: Fight the Kilrathi.
WC4: Fight Conspiracy.
WCP: Fight the Bugs(Stand in for the kitties.)
So, more or less... the next full-length retail WC game should be a "Fight the conspiracy" game. Perhaps...
Kilrathi factions are being randomly attacked by Confed fighters. In response, the Kilrathi once again begin to band together, and prepare to put a stop to it once and for all... by destroying the Confed fleet. You are either placed in a position to get to the bottom of it(Col. Casey?), or are dragged along for the ride, fighting out battles and trying to do some good. Eventually the bad guys are revealed.(something similar to the Black Lance theme, though not genocidal towards humans... genocidal towards those loveable fluffy kitties!) The "bad guy humans"- possibly based out of a carrier that mutinied, kind of like the Gettysburg- or even better, a full carrier group- are working to incite a new war, to convince Confed to wipe them out, once and for all. (motivations: Hatred, a la Hawk. Perhaps an old warhorse that just can't sit back and let the kitties become busom buddies with Earth?)
General mission structure:
Mixed, carrier defense from enraged kittens, protection of kilrathi convoys from rouge pilots, assaults on "bad guy" carrier group... and so on...
Come to think of it, this wouldn't be a bad mod.