It's hard to separate G2 from G1 as they share so much in the cartoon and toy lines.

I would have loved to see a lot of the newer toys pop up in the fiction. The rotor force and laser rods showed up in the comic but many of the others never got a chance, most likely due to the abbreviated comic run. With many older characters being killed off there would have been some space in the ranks and I think the darker tone of the comic could have introduced some interesting character dynamics. The cartoon was just reruns of the G1 series so that was never going to happen there.

IDW have continued the G1 comics with Regeneration One, maybe we'll get Regeneration Two some time? *fingers crossed*