I believe the short answer is that Megaman 5 and 6 were both released after the SNES and, more importantly, near the end of the life cycle of the NES. Don't get me wrong, they were still releasing games for everyone that stuck with the NES, but companies will limit production for almost any game for a console close to its end. There might be way more to this story than this though.

Also remember not to mix monetary value and actual rarity. If I needed to guess, I would say 6 was produced in lower quantities than 5, but people tend to like 5 more, from what I've heard.