The scenario has MegaBlaziken attack that turn he's hit, so Endure is not used. Even if it did use it, Blaziken then can't attack and is an easy target for Mewtwo.
Let me start this scenario over.
Turn 1: Blaziken uses Protect. Mewtwo has no moves that boost its speed. Blaziken will now outspeed Mewtwo regardless.
Turn 2: Blaziken uses Shadow Claw. Mewtwo takes Super Effective damage taking out at least half its health. Mewtwo uses Psystrike. Blaziken holds on with Focus Sash. Mewtwo has no priority moves.
Turn 3: Blaziken uses Shadow Claw. Mewtwo fainted.
Here's another scenario where both have Substitute.
Turn 1: Mewtwo transforms into MegaMewtwoX and uses Substitute. Blaziken uses Substitute. Both are at 75% health. Blaziken recovers with Leftovers to 87.5% and gets a boost in Speed. Blaziken will outspeed Mewtwo.
Turn 2: Blaziken uses Shadow Claw. Mewtwo's substitute vanished. Mewtwo used Psycho Cut. Blaziken's substitute vanished. Blaziken recovers with Leftovers to 100% and gets a boost in Speed.
So here we are at turn 2, where Mewtwo has 75% health while Mewtwo has 100% health and +2 to his speed. If Blaziken uses Shadow Claw, that will be enough to either outright kill Mewtwo if the RNG favors the attack or if the high critical-hit rate comes into play. Based on who has better prediction and luck, the two are evenly matched, but Blaziken very much has the chance to win.
So yes, a regular Blaziken going toe-to-toe with the
Mega forme of Mewtwo and outright winning against a regular forme. OP.
Considering how overused Mega Blaziken is going to be, I can already guarantee that people are already setting up Trick Room and Substitute teams to counter said speed boost. After a few months, nobody will want to use it.
As for the 2HKO Mewtwo...that doesn't make sense. Sure, it would survive one Psychic thanks to a Focus Sash, none if it doesn't hold it, but even then, it has no chance of outspeeding it on the second turn as a Normal Blaziken as Blaziken's base speed stat is 80 and Mewtwo's is 130.
Also, how is Mega Blaziken going to hold a Focus Sash when it has to hold the Blazikenite to transform? One more thing, the thought of outspeeding Mewtwo on the first turn wouldn't work because if Mewtwo became Mega Mewtwo Y and got a speed boost on its already 130 base stat, there's no way Mega Blaziken would be able to outspeed Mega Mewtwo Y from one single speed boost.
Blaziken will be Uber again, meaning illegal to use in regular battles outside of legendaries like Mewtwo or Kyogre. Even if it is within the regular OU play, people will not pick up on Trick Room and Substitute simply to counter one Pokemon. The metagame doesn't work like that. Unless Trick Room teams themselves become more viable, they will not be more used, otherwise the one guy not using Trick Room or Blaziken is suddenly winning against all the Trick Room teams, which is completely counter-intuitive to using a set team like that in the first place. Scizor is the most used Pokemon in the metagame, yet people don't make sun-teams exclusively to counter it. That will get them curbstomped by any other weather team, or worse yet,
by the opponent switching Pokemon.
And regular Blaziken gets Speed Boost in the Dream World. Did you not know that? Hence, Mega Blaziken is not even necessary and at times may even seem inferior to regular Dream World Blaziken, which will be accessible in X&Y due to how Pokemon Bank will work.