for me, that was funny. sirion had multitude of ways how to finish off fontan, and those religious takeovers were completely irrelevant in strategic way, i could even say that they somewhat added to roleplaying feel. on contrary, once rto's were crippled, we only saw "go to region a, take her - than go to region b and take her as well" mood which is everything but funny.
I don't recall any specific instance of RTO ability being nerfed. Not that it didn't happen, but I just can't recall any specific changes that would have caused that. Do you remember any details about what the change was?