You know, all they had to fucking do was just have an episode where their grandpa is forced to come out and tell them that they actually aren't cousins, and the only reason he kept that lie going was so make sure they watched out for one another and didn't get distracted by hormones, BUT THAT PLAN WAS OBVIOUSLY FAILING IN THE LATTER REGARD.
They wouldn't have had to redesign characters, or change animation styles, and they could have kept building on that rather impressive canon that they were establishing so much in the first seasons, AND they could have played around with character development and relationship drama and sexual-but-not-too-sexual tension elements whenever the alien action stuff died down.
From what I recall, in the pilot Ben and Gwen weren't even related at all (classmates I think) anyways, which is why a lot of those awkward "wait a second, aren't they supposed to be cousins?" scenes ended up happening throughout the early series.