I haven't had enough Ike vs. Mewtwo battles to really give meaningful input yet, but I do use both of these characters the most out of the roster.
My initial gut reaction is that Mewtwo can now play footsies with Ike due to the massively buffed walk/run speed and lightning-quick Dtilt. If Mewtwo can land a Dtilt, he can easily take Ike from 0-57% at least. That's about halfway to kill % off one combo. Never forget that, depending on the stage, Mewto's Uthrow is a kill confirm at some point past 100%. I don't know the exact %s, sorry. Ike is heavy, so that increases the usual kill % I'm used to worrying about.
Meanwhile, Ike can kill Mewtwo super early, especially off up throw combos and reads, or Bair near the ledge, Eruption 2-frame reads, randy Usmashes, etc. Ike can end Mewtwo rather quickly, and nearly all of Ike's best options are out of Dthrow or Uthrow, so Mewtwo players have to be on-point in neutral, watch their spacing, mix things up, and NOT linger in shield.
In the air, Ike can out-range Mewto most of the time, but Mewtwo's Nair has an incredibly long-lasting hitbox(es) than can easily punish air dodges and lead to huge combos. Mewtwo has a long reach in the air as well, with Fair, Bair, and Uair all reaching out a good bit, and comboing into each other, depending on %.
Shadow Ball can lead to a lot of cheese vs. Aether (in other words, free %), so Ike mains need to be on-point about mixing up recovery and sweetspotting the ledge as best they can. Mewtwo's Dsmash is very powerful and hits below the ledge, so it is basically like Ike's Eruption in that it is a fantastic punish for ledge snap recoveries. Sharking Mewtwo under the stage with Aether is important, but you can't do it all the time for fear of eating a Shadow Ball.
Mewtwo's Usmash can catch you on the ground, and tends to suck people in. While it is every bit as laggy as Ike's Usmash, its hitbox lasts even longer and is stationary, so it can be deceptive and pulls you in from weird angles. Due to Mewtwo's massively buffed running speed, sliding Usmash now slides A LOT, which can be a big problem for you guys if you are above Mewtwo.
Due to Mewtwo' speed increase, I would think Ike's falling Bair/ SH Bair are even more important.
I think Ike has a much faster grab than Mewtwo, so pivot grabs from Ike are very important, as well as using grab to punish. All of Ike's scariest conversions are off of grabs (and aerial hits in general).
Ike's dash attack is great for neutral punishes, and has a crazy range, but Mewtwo's dash attack is lightning-quick!
Finally, even though Confusion does not combo into anything for Mewtwo, it has just as much range as Ike's Fair does, deals 9%, and resets back to neutral, so it can be annoying if the Mewtwo player is better at aerial spacing. On the ground, if you don't react fast enough, this can lead to a jab lock, Disable, and a free smash attack or throw for Mewtwo. BUT, if you react fast enough, you can get out of it having only taken the 9%.
All in all, I would say the matchup is much more even now.
Once I have more matchup experience, I think I will be able to offer better advice. Cheers, fellow Ikes. Also, give Mewtwo a shot if you haven't already and you want a second/pocket character. Mewtwo feels much, much more fun than he did before.