Hmm, well I commend your efforts in trying to objectively determine power levels by abilities alone, but that simply doesn't fully convey the full power of the characters. Take The Kid(IWBTG) for example. He has no powers or abilities except for a double jump and a tiny little pistol. But he's a badass.
I agree that the difficulty of the games should play some role in determining their respective powers, but even then we can only say that Quote and Megaman are at least as powerful as their respective games (necessary condition). For all we know quote breezed through the entire game and crushed Ballos without taking a hit while Megaman just barely scraped through his levels, or vice versa.
The only skill levels of the characters that we can be absolutely sure are cannon are those in cutscenes, and even then, those could have just been an off day for the character, or a point in time where they were feeling extra destructive. Their Inner strengths really can't be determined.
On the other handwe all know that if we were to put both Quote and Megaman in a fighting game together with some subset of their respective abilities, it would quickly become apparent that one or the other has the edge in combat, when controlled by a wide variety of players in a range of skill levels. And to be honest, that's what most people mean when they ask "which character is stronger" anyway.
Come to think of it, It probably wouldn't be to hard to throw together a game like that, with just one stage and only Quote and Megaman as fighters. Hmm...