@Joseph Raszagal  
The question is “bigger”. Not “more evil”, “more competent”, “more entertaining” or “more villainous”. So I think it’s a legit answer. :-) (And would still be legit if the Master was in a normal humanoid regeneration.)
 
I think, however, that the Master is a better villain. Discord as a villain is kind of dull precisely because he doesn’t have any kind of master plan most of the time; he’s in it for the lulz. He’s an incredibly entertaining character, but, like Q, he’s better as an annoying asshole acquaintance. Because when he’s a villain, you know he will lose, because he’s much too powerful to be truly villainous and still be needing to pull Xanatos Gambits. But if he might be manipulating you into doing the right thing by being an ass, then you actually don’t know if “defeating” him is winning against him or not.
 
In my original take on Discord before Season 4, he was Q, and his entire mission on Equestria had been to eliminate all traces of the racism that persisted from the pre-Windigo days by destroying society so thoroughly no preconceived pattern could survive. He took on the role of the avatar of disharmony because the key to Equestria’s evolution is harmony, and Q often takes on the role of antagonist to push a species in the direction he wants them to go. But then they put him in stone, and it had the same effect as the Continuum binding “Quinn” into a comet, so he couldn’t get out. By “Return of Harmony” he was basically thoroughly pissed off, and even though his mission had actually succeeded eventually, the personal cost to him was high enough that he decided to screw with them just because he was mad. (Kind of like what he would have done with the Calamarain if Q2 hadn’t intervened.) Season 4’s kind of shot the whole idea, but I still think Discord works better as chaotic neutral than evil. Keeps you guessing.
 
So I’d say the Master is a better villain, even though I like Discord better as a character.

I mean, if we’re strictly talking size, it isn’t even a competition.
 
But villainy? Discord seems pretty evil in the Discorded Doctor Whooves universe, but gotta keep in mind, canon Discord is reformed. Then again, the last thing that the Master did in his own canon series was take a BIG one for the team by stopping the Time Lords from coming back and going down with them.
 
Hmmm… this question is harder than I thought it’d be.