As someone who loves the GT3 FXR [and the whole iTCC thing], likes the GT3 XRR and despises any kind of FZR in existence, I propose the following ideas.
1)
At the start of the series, each competitor is given 12 "credits" [2*6, taken as an average across all rounds]. We have a round at each of the LFS environments [6 of them]. At each round, the cars are ranked in terms of their pace and given a credit "cost". eg at Westhill, the XRR would cost 3 credits, the FZR 2 credits and the FXR 1 credit. Thus the fastest driver would still win, those who like the iTCC thing still get their FXR racing and those who hate shopping trolleys could still get their RWD fix. And hey, awesome people could try and win at Westhill in the FXR, just for lulz. Newcomers to the series mid-season would be given 2 credits for each remaining race -1 so they don't enter just to get the awesome car for a certain round.
2)
A similar vein to the one above, but STCC style. We have a "Front", "Middle" and "Backmarker" car each round, and so multipliers for the points depending on what car you're in. eg at Westhill you might get a 1.5x points bonus for driving an FXR.
The problem I have, particularly with the GT Series style, is that it screams "tyre saving" to me. The beauty of the iTCC is that it's all about everyone going completely flat out for 15 laps or so, which is why everyone loved it so much. Putting mandatory rounds in other cars would I think put lots of people off, and we'd end up with basically a sprint version of MoE with just all the pro people in.
Just my 2 cents.
EDIT: I'm not in any way saying the GT Series was boring - not at all - but it's just not the iTCC.