Interesting choices. I like how you guys did it similar to your "best Batman villain" and eliminated the obvious choice. I wonder how much of a person's preference is related to what they read when they were younger. For example, my favorite characters are Cable and Rachel Summers. They may not be the best or most interesting characters, but as a kid I thought they were really cool, so they are still my favorites (especially within the past couple of years that series where Cable and Hope are running away from Bishop by hopping through time).
This might have been mentioned in the other thread, but there's a pretty good argument for Cyclops if you look at him as being one giant arc that ends with the end of Avengers vs X-Men. In short here's a guy who started out young and idealistic, and placed in charge or the team. Over time he sees that "dad" (Xavier) is kind of a jerk, people he was responsible for die (including his wife, repeatedly), and large-scale genocide committed against his people repeatedly (Mutant Massacre, Genosha, end of M-Day). Because the rest of the Marvel heroes don't care he becomes increasingly insular and cold. This culminates with AvX where he goes nuts almost destroying the planet, but in the end mutants are saved. And here's where it gets really good: given the choice, he would do it all again, even with the death and destruction, because it saved his people. He went from that young idealist to out-Magnetoing Magneto, the 1st villain the X-men ever fought. It would be almost perfect if Marvel just stopped all Cyclops stories now and let the character fade away.