My opinion tends to fluctuate a bit, but I am generally around 50-70% confident that he will be in the game.
There are many reasons why he has good chances of being in the game. I won't explain them all  in detail now (I imagine you've heard a Mewtwo fan list them all before anyway, haha :D) but the main points are:
>His massive worldwide popularity - notably, he is very popular in Japan as well as in the west, unlike Ridley, who is massively popular in the west but not particularly popular in Japan. It's possible that he's currently the most popular character worldwide who is yet to be confirmed for Smash 4 (although it's very close and difficult to judge between him and King K. Rool).
>His recent huge boost in relevancy in the Pokemon series is a great factor in his favor, considering Sakurai has said in the past that this influences which Pokemon he chooses for Smash.
>The fact that he has been planned for - or included in - all SSB games so far (that includes Smash 4, if Sakurai's "We're thinking about it" comment is accurate).
Overall, his CV for Smash 4 is perhaps the most impressive of any character not playable in Brawl.

However, although it looks great on paper for Mewtwo, what holds my expectations down a bit are a couple of very simple theories that may or may not hold any weight.

#1 is the dreaded "slot rule" - while I don't believe this really matters much (if at all), some believe that Pokemon cannot have more slots than Mario. Although Pokemon had more characters than Mario in Brawl (6 compared to Mario's 4), it had the same number of slots on the character screen (due to Pokemon Trainer being a 3-in-1 character), and so Pokemon has never actually had more slots on the character select screen than Mario.
As this "slot rule" hasn't been broken in the past, Sakurai may indeed follow this rule - but in my opinion, Fire Emblem's treatment proves that you can't judge patterns by two or three games, and Sakurai might feel that Mario can stand to have one less rep than Pokemon because it has the extended Mario universe to represent it as well (Yoshi, Wario, DK and Diddy Kong, while not really Mario reps, still represent the Mario universe to a certain degree).

#2 is the simple fact that Sakurai said that Brawl's roster was close to the limit of what he felt could be achieved, and that we might end up with fewer newcomers this time around. With many expecting the roster to be around 50 (if that), having six Pokemon characters - while possible - is certainly not guaranteed, and I feel that Jigglypuff would most likely get in over Mewtwo if only five Pokemon reps made it in the game.

#3 is that some feel that Mewtwo doesn't provide enough variety to the Pokemon roster, as Lucario and Greninja are both humanoid, "cool" Pokemon with chargeable neutral-B projectiles - like Mewtwo. Additionally, Mewtwo's potential to be unique by utilizing his mega evolution  has taken a hit as Lucario and Charizard both already provide that.
However, in my opinion, I feel like Mewtwo's psychic abilities are enough make him a unique fighter, and his moveset could just be redone to further differentiate him anyway. Also, his mega evolution could be designed to work differently to Lucario and Charizard's, it doesn't necessarily have to work in the same way. Assuming Jigglypuff comes back as well, then I feel like the "cute" side of Pokemon will be represented quite well, and the Pokemon selection would still have good variety if Mewtwo rounded it out as the sixth Pokemon rep.

I'm sure that there are more arguments as to why one might doubt Mewtwo's inclusion, but those are the main ones I can think of. I don't really agree with most of those arguments against Mewtwo, but even though it's easy to come up with a counter argument to them, we never know what Sakurai is thinking, and thus these arguments against Mewtwo could indeed hold some weight.
So yeah, overall I guess my view of Mewtwo is that, while I am given confidence by all the factors in his favour, I have a big shroud of doubt due to the possible reasons why Sakurai might decide not to include him. Chrom's treatment has proven that characters don't just get in because they are popular. I do think that Mewtwo is close to guaranteed if there ends up being character DLC for the game, though.