CC had actually more than implied Warren and Jean more than once. Once during the Byrne era with Warren saying "looking good red" and she kisses him...
Yea exactly, the 97' incarnation even involved the Morlocks and Mr Sinister to further solidify the comparison, so it's definitely taking inspiration...
I'm pretty sure the main motivation was Marvel trying to portray him as wrong during the era, hence "Cyclops was right". It also picked up after AvX...