It's cute that they want to involve the players, but I feel there are other ways to do that.
For a Mega Man game, this is the best way to involve fans into the project. Fan feedback can work if is not too forced into the development of the game, and after all this years we don't want a bad game because of bad decisions made by "fans".
Edit: Y'know I totally misread your post I think. Minus the part about agreeing that this the "best" way to involve the fans. I'm striking my first sentence but keeping the rest in play for the sake of argument.
As I've mentioned before there's a huge difference between letting the fans choose something minor, yet cool; and something that effects the entire story...like the heroine's design. A character's design, like Dice pointed out, is reflective of that character's nature, role, and can often be symbolic of something later within the story. Choosing the heroine in this way invalidates anything relevant to her design because they're just going to plug her into a predetermined role that may or may not fit their look.
Now if you want the best way to involve fans in the project there are many, many others that are far less plot altering. Like:
-Choose the design of the first ruin's Reaverbot boss!
-Choose the design of Tron's new Gustaff Mark 3!
-Choose the design of the new Flutter!
Ect. Those are major decisions that would make the fans feel like they're apart of something special without putting the game's story value in jeopardy before it even begins.
Taking an old RPG for example, imagine if say...Final Fantasy 7 had a similar contest for Aeris. And instead of the cute looking flower girl the fans chose as masculine, muscular girl who looks like she just walked out of the portal of darkness for that role; and not one bit of dialog or story was changed.
It would be laughably ridiculous. Granted this scenario isn't as extreme as my example but the principle is still there.