I think as previously said the only ones that could pose difficulty is the high tier Legendaries.
Mew - Mew actually was able too run with Mewtwo, even if they did it to add "drama" which I wouldn't take Mew lightly since Mew is pretty much Mewtwo dad, since his DNA was used to make him.
Lugia - It took on the Kanto bird Trio by itself. With a little help from Ash and Co. I think Mewtwo would have a quite a fun time trying too get past this fellow Psychic type. If Lugia was able to land an Aeroblast, then it wouldn't look too good against Mewtwo.
Ho-oh - I don't think I remember seeing anything from it battle wise. Every time I remember it, Ho-oh was mentioned in a mythical sense. Since it was opposite of Lugia, I would only assume since it is the Trio Master of the Dogs that it could pose a threat to Mewtwo.
Celebi - If we are going to use the Time argument with Dialga then Celebi would be in that same discussion as well. Since Celebi is also the time people. Celebi could go back in time and kill all the scientist before they created Mewtwo, but that wouldn't really show his capacity vs. Mewtwo in an actual battle.
Lati@s - I don't really see the as upper tier legends first off. Tobias Latios tied with Pikachu, and Nurse Joy Latias didn't far that great against Forrest Rhyperior.
Kyogre & Groudon - Both are both incredibly powerful pokemon, seen through there battle vs. each other. I could see them giving Mewtwo a challenge.
Rayquaza - Like the rest of the Weater Trio, they are powerful, but I don't see them beating Mewtwo at the end of the day.
Jirachi - I suppose it could wish Mewtwo to die, but still that doesn't showcase its combat capacity vs. Mewtwo.
Deoxys - It would be interesting to see this match up, if anyone would give Mewtwo a fight it would be Deoxys.
Dialga & Palkia - They control both Time and Space respectively, so yes if they use those aspects to go back in time or warp the spacial area were Mewtwo is at then he could be defeated.
Heatran - I am not seeing them, does not seem like a high tier pokemon first off, I haven't really seen anything from it that would warrant me to think it would be able to stand up against Mewtwo.
Regigigas - Yes this is a trio leader, but I don't really hold much value for Regigigas, I don't see it beating Mewtwo.
Giratina - Mewtwo has Shadow Ball as his signature move does he not? I don't think that the typing with deter Mewtwo, it would be an interesting fight either way.
Cresselia - Like Heatran, I haven't seen anything that would make me thing Cresselia would even have a remote chance at beating Mewtwo.
Manaphy - Every time I have seen Manaphy it was just with May being a baby, so I really can't say much for it.
Darkrai - Tobias Darkrai lost to Sceptile. Even if it faced four others prior, it still lost none the less. And Mewtwo has Focus Blast, so typing again is not the issue.
Shaymin - As with Manaphy I have yet to see Shaymin in a fight.
Arceus - Yes this is said to be the creator, but in a battle would it be able to beat Mewtwo?
