As it stands, in the poll for 'which series needs to be retired most,' Megaman has the least votes. People would rather be rid of Final Fantasy, Madden, Mario, Pokemon and the Sims before Megaman.
So while in the classic series megaman would always best Wily, Bass never was truly destroyed, and when we travel to the future, X eventually gives up and retires, or becomes a cyber elf, while Zero takes a leave of absence but still comes back to save the day. I think since Zero died with his boots on, fighting for a cause he believed in, Wily made the better robot, instead of the blue bomber who decided to give up.