Mystique and Destiny were suppose to be lovers, though I don't think anything was officially stated. Readers were meant to read between the lines on that one.
Sorry, Montoya's transformation into the Question ruled. Also I wouldn't call the Question one of their most beloved characters. Its not like they made Wonder Woman gay.
I hate that Montoya is The Question as well. Why do all female heroes have to be just another version of a male hero. Batwoman, Batgirl, Supergirl, Mary Marvel, etc.
Personally, I think The Question is an interesting character who didn't need to experience a revamp.