I know this has already been discussed like...a billion times...
But I don't see it, I don't see why Doc has an edge over mario. Mario's inability to KO is the only thing Doc has over him, and his KO ability isn't even THAT bad.. Mario can combo and recover much better. I know there are little things like Doc's Bair edgeguard and long(wide, whatever they say) cape that reaches under the ground that tip the scale, but Mario's Bair does more damage and his utilt off-set that. I see them as pretty much equal.
In practicality Doc's juggles are just as good as Mario. In fact, really the only five things Mario has over Doc are:
1. More launchers with Fair
2. A spike of sorts
3. Better recovery (I include the walljump here)
4. 3 frames less lag on select aerials
5. Fsmash with more range.
Now then, you can kind of rule out 1 and 2 because they trade off with KO ability that Doc gains from his fair. Better recovery is there but not game-winning, really, and unless you are M2K, 3 frames of lag isn't that much at all. Oh, and the fsmash has its moments but it has a sweetspot that can be awkward for Mario and is still fairly stunted in range compared to other characters. At least Doc can use his Dsmash as well as his Fsmash.
Doc has a better defensive and pressure game with pills/dsmash, better edgeguarding and stronger KO moves, his own juggles that Mario doesn't have (usmash juggles) and more options out of a grab. Oh yeah, and a slightly better jab game at that.
Any decent player will tell you Mario has trouble applying pressure more than the other characters up there do (hell, even Ganon does better).
Like I said, I love playing both characters, and it isn't like either dominate in the metagame, but Doc does have advantages that outweigh Mario's.