Mega Man wins by a landslide. Not only did they do the most milking, but they had the least amount of changes between games.
What are the differences between Mega Man 1 through 6 on the NES? How many games had 6 installments on the NES? We had 3 Marios, 3 Castlevanias, 2 Contras, 3 Dragon Quests, 3 Final Fantasies, and I can't think of any franchises that got 4 or 5 NES installments off the top of my head. Can anybody else? I'm just drawing a blank, but right now off the top of my head it looks like at its debut it doubled the other big NES franchises.
Sonic is a close 2nd. Mario's been around since 1981, Mega Man's been around since 1987, and Sonic's been around since 1991. Both Mega Man and Sonic already have more games than Mario, whether you count only main franchise games or all cameos and spin-offs.
Mario games all have huge differences. SMB1, 2, and 3 are all completely different. 2 had vegetable picking/throwing, superjumps, character selections, and that crazy potion dimension. 3 had flight, different suits (tanuki, hammer bros., raccoon, frog), giant land, pipe land, a world map, and multiplayer minigames.
To say Mario was milked more than Mega Man is just... insane. Please, somebody provide a serious argument that does so, so I can utterly destroy it.
(Also, just so you all know, I've played both Mario Strikers and Mega Man Soccer to their completion. This is very important for my credibility.)