From what I understand (I'm a little behind on the comics) Computron didn't appear in Combiner Wars, and nor did Bruticus (who has only just turned up in the Til All Are One series). So just because the combiners are produced doesn't necessarily mean they're included in the comics (though no doubt Hasbro would like them to be).
As for story, we could go back to being at war, with the Decepticons having possession of the Enigma of Combination and going a little nuts with it.
Another Prime (Onyx, perhaps) could turn up and recruit those with animalistic alt-modes to his army. He was once allied with Nexus Prime, so might have some insights into combiners.
There's heaps of room there for story.