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The gripping X-Men: Evolution animated series adopts a slightly different perspective on the X-Men as compared to the conventional lore. As discussed in this post, the series tinkered with "the age of X-Men characters, making most of them teenagers" and enrolled in the Bayville High School (with Mystique originally disguised as the Principal of the school, in Season 1).

The first episode of Season 2 is epoch making, as the Brotherhood of Mutants decide to "come out", revealing their mutations to the public. During the process of neutralizing their offense and saving general public from the destruction they unleash, the X-Men teenagers end up revealing themselves too, much against the desire of Prof. X who has been believing right through that the X-Men better stay disguised till the society at large is ready to accept mutants. With no choice left to prevent the mutant unveiling, Prof. X decides to take the extreme step of using his powers to erase the event-memory of everyone present at the venue:

As we see at 18:44 in the above clip, Prof. X successfully erases the memories of all-but-one of witnesses, finally attempting to do the same to the new principal of the school, Edward Kelly. Upon attempting the same with him, the Professor encounters some sort of resistance, or a psionic burst, as a consequence of which he passes out.

Clearly, it must have been a powerful mutant disguised as Principal Kelly, with psychic powers comparable to Prof. X, or perhaps even superior. However, apart from Prof. X, the only psychic mutants revealed in the series who could fit this description, were the teenaged Jean Grey (who was both an ally, as well as affected party here), Lucas and Mesmero (who showed up only later in the series). (Note: Apocalypse still hadn't woken up until this point in the series.)

Until the end of the fourth season, after which the series stopped, this arc of the story was unexplored. All we got to know of Principal Kelly's character description can be succinctly summarized as:

Edward Kelly was the second principal of Bayville High (the first, Ms. Darkholme, aka Mystique, had vanished) and carried suspicions about the mutant teens which became full-blown prejudice when they were publicly revealed, causing him to make reforms at the high school. Later, he ran for mayor of Bayville competing with the falsely heroic Brotherhood for media attention, a nod to his career as a politician in the comics.

So,

Which powerful mutant was disguised as Principal Kelly of the Bayville High School?

As dull as it sounds, I'm not entirely sure there's actually a mutant behind Principal Kelly... Although if there had been, it might have been Mr. Sinister.

First because Kelly's comicbook counterpart is a major anti-mutant character.

More reading on his marvel.com page, but while obviously 30+ years of existence will have seen the character switch sides at times, the guy is still your default anti-mutant antagonist. He's been adapted this way in animation (the original X-Men animated, X-Men Evolution, Wolverine and the X-Men...) and movies (the 2000 one). Most of the time, the guy isn't a mutant himself - X-Men (2000) being an exception, and that was a forced mutation.

Sure, it could be that someone else entirely is posing as Kelly, but...

In-universe, Xavier doesn't seem to think Kelly is a mutant.

When Xavier wakes up after having passed out, Wolverine tells him he pushed his brain to "overload". Xavier doesn't refute it, and later states that he's "not sure he finished the job" (with Kelly's memories). Note that at no point, he mentions the possibility of Kelly being a mutant himself; if he believed such a thing, I'd expect him to drop something along the lines of:

Kids, that school principal of yours somehow blocked my mental fuddling. I suspect he might be a telepath too, so be extra careful, because a telepath could uncover your identities. I am even more tempted to think something's iffy, because your previous school principal was an enemy of ours, so you know, let's double our vigilance just in case.

Then because the writers never did anything with Kelly's character.

The writers had three seasons after that episode to start a plot, and apart from the occasional "oh my! Does he know? Was his memory not wiped correctly?" moment, no serious subplot seemed to be on its way. The scarce info available on the cancelled fifth season doesn't point to such a thing, either; rather a "Dark Phoenix" arc. Kelly, not so much.

MARVEL ANIMATION AGE: Was anything beyond Phoenix planned for season 5?

BOYD KIRKLAND (producer/writer/director of the show): We never knew from one season to the next whether or not we would get renewed, so it was difficult to plan very far ahead. And once the network made a decision, we usually only had a few weeks to develop ideas before going into production. So no, we didn't do any serious development for season 5, beyond sketching an outline for the network of the Jean storyline and indicating the general direction we'd like to take the series if they gave us a pick-up.

_{"Boyd Kirkland Talks X-Men: Evolution"}

Bit of a stretch, but they might have brought Mr Sinister into it.

From the above interview:

MAA: An odd question, but given the big build Apocalypse received throughout the series, were there ever any plans to introduce Mr. Sinister in the show?

KIRKLAND: I think his name came up a time or two, but we were concerned about getting too many big baddies going on at the same time. We were mostly doing smaller, character driven stories, while planting seeds for the bigger epoch action stories which finished up each season. With the Apocalypse arc finished at the end of season four, we might have been able to bring him into the fifth season, but we never really had any serious discussions about it.

_{"Boyd Kirkland Talks X-Men: Evolution"}

Mr Sinister has been given both shapeshifting and mental abilities in the comics. They could have had him posing as Kelly for whatever reason, but that's really speculation, given that season 5 never made it.

None.
Prof X just overloaded himself (as Storm warned him that it's too much even for him).
And as Prof X state later he fainted when he was inside Kelly mind and was (probably) not able to wipe up his memory fully.