@ Real Cal, hey hey, I'm going to take any excuse to have Yukari appear in a nurse outfit. You know what, screw it, shifting my vote entirely to Mewtwo because Mindhax!!
Okay in all seriousness Fate's right although typically it's because it boils to the same thing, time ot get started
@Fate
Comparing our feats here with the superpower wiki may seem like it happens a lot but it doesn't really. Anyone who does that is shut down instantly since we're smart enough to acknowledge that Yukari is not an omnipotent lady capable of flipping those types of boundaries with no issue (Although I sure would love to wank on that one).
Anyway I'm checking Mewtwo's page but.... Yukari has been shown to be resistant to illussions. The lunatic rabbit's and especially Keine's temporal hiding. This is the same one that worked against others who are already resistant if not immune to Reisen's insanity inducing and illusions. Alongside with casually shrugging off Reimu's illussion too which is a higher scale too considering it's summoned by a god, and it's not some lowly god like the Aki sisters. Add in the fact that Yukari could 'program' powerful shikigamis with ease. Those are already helping factors against mind control or mind haxx. Now I have to ask, can willpower shake off mind control in Pokemon? Or extensive knowledge? Because that could be effective too.
Yukari has shown the potential for time travel, although I won't go too far on that regarding the spiriting away working on Maribel and sending her centuries in the past when her ability is really just the weaker form. So that handles the issue of time travel but then again I doubt you allowed either, and no it's not wank, I'll bring you the proof if you feel like. Or you know just check out Maribel's profile in the Touhou wiki.
Power Mimicry may not be so successful considering the complexity of Yukari's power. Since boundary manipulation has been explained to be such a confusing yet dangerous ability. In fact a weakness though of on the super power wiki, which is actually common logic so no need to be worried about me 'borrowing' a feat there, is that having this power means you'll have to be experienced and knowledgeable on how to use it. Mewtwo however could be smart enough to use it however but in the end Yukari's expertise should easily counter Mewtwo's attempts to use that ability. Her power is still very versatile and if I remember it can only copy the first move, and Yukari can just return the attack probably. Or negate it with her own ability. That said Yukari has to be moving 'after' Mega Mewtwo so this could play into a mental wits if Yukari figures this out and sends out weaker abilities or something that would be detrimental to Mewtwo, ex a healing ability (although I doubt she can do that) or an ability she could easily reverse back. Of course they have speed equalized so.... not sure how that comes into play with that so I'm going with the wits idea.
Reality warping, teleportation, and flight are shared by both.
Psyche up is not something Yukari really uses but it would be interesting to think of regarding Yukari's err, pillow soft body yet hard enough to pierce?
Yukari... I'm willing to argue something is up with her and telekinesis regarding Sumireiko but I'm not sure. If she doesn't even deem her a threat, someone who can make mini black holes (which aren't real black holes), psychokinesis, and elemental manipulation, I don't think she's gonna have troubel with those kind of abilities either. And it's not scaling if it's outright said that Yukari literally had no care about what happened in the previous incidents and didn't act all during those times.
Precog is kinda shared by them, which is furthered boosted by Yukari's 1000 variable count and capability to trick others. Her batman of gambits triumphed over batman of gambits over batman of gambits. Such as tricking the Scarlet crew into going to space as a decoy, tricking Toyohime to thinking she's the main force, tricking Eirin into thinking alongside that too who led the creation of the moon and is known to be knowledgeable if not related to the goddess of knowledge (questionable so don't hold my word on that) and overall tricking the lunarians into thinking they won alongside even confusing the super genius Ran who should be close to Mewtwo's level of intelligence.
Overall, this is why Yukari should win. She has the advantages overall on those cases. Very versatile, alongside knowledge of Batman Gambits triumph. Even if you take away a few of the above points, Yukari still has a lot of advantages. If you think some are 'untrue' then I'll do my best to prove why it's legit.
Also yeah just basing this on Mewtwo's profile
Edit - Also glad you pointed that out Fate (Although there goes Tier 0 Yukari) this should clarify most things. But then again that's only to be used as a reference point, nothing to really copy everything.