When Mewtwo Teleports, at the end of the Teleport he has a "twirl" animation. When Mewtwo's Teleport ends in the air he also has this twirl animation and then when he lands he gets ANOTHER landing animation (double lag). This is why teleporting in the air on top of the stage is mostly always a bad idea.
It is possible to Teleport at a range where Mewtwo is still in the air but his twirling animation makes him land, this will cancel the twirling animation and initiate the landing animation. The landing animation is shorter than the twirling animation, it also allows Mewtwo to "slide" briefly.
It is possible to Teleport at a distance where the twirling animation is not even seen (cancels frame 1 by the landing animation), if you are able to do this then you will have less lag. This is kind of hard to do consistently though and the lag is still there (it's just a little bit less), it mostly happens when you teleport perfectly above the ground or teleport in a perfect diagonal.
So to answer your question: Yes, there are ways to have less landing lag when teleporting into the ground (although it's slightly less lag), it's a distance/angle relation that I honestly don't know that well.