Dr. Wily as a character has always been weirdly complex especially since he has multiple different goals and ideals. His primary goal has always been to satisfy his ego by dominating the world and humiliating Dr. Light, but he has a lot of different philosophies attached to that:
1. Dr. Wily believes robots are just tools and should never have been given intelligence, both for ethical and practical problems
2. Should robots necessarily have intelligence, Dr. Wily believes they must also be given freedom and not be stuck in limbo of service, this is because he believes that robots in servitude are inferior in performance to robots with freedom
3. Dr. Wily doesn't believe that robots with sentience will be capable or treated as equal to humans and giving them sentience without freedom only creates conflict
4. Dr. Wily's loyalty is foremost to himself and his goals of fighting Dr. Light, but he is also loyal to humanity as a whole with or without robots; he doesn't want to bring the overwhelming calamities or genocides seen in later Mega Man games after his death
At least that's what I remember from Dr. Wily, actual details will change depending on the time, media, and person you ask since most of this is vaguely implied at best.