I've played Mewtwo a fair amount, love him, and have some play-tested suggestions.
1) The trick with Mewtwo is getting the energy on him. Preferably, this happens fast. 4 Max Elixirs are a must. You also want a second Mewto set up on the bench, so 3-3 Inkay/Malamar is a wise call, along with 4 Ultra Balls to get the energy into the discard pile for Malamar. 1-2 Sycamore (instead of 1-2 N) is also a good play to get the energy into the discard.
2) some advanced options:
- 3 float stones - you can keep Mewtwo on the bench and load him with Max Elixir and then float the Active out, especially for fast starts.
- 3 Choice Band and 1 Fury Belt - Mewtwo's GX attack is strong, but can benefit from a little help on Golisopod, Zoroark and some of the other 210 HP mainstays. Buzzwole is rampant in the Meta, and you have to get to 100 damage for the IHKO (weakness). Mewtwo GX needs 3 energy on him - that's the key.
- baby Mew - same attacks, but you only give up 1 prize card
- nest balls given all of the basics, and maybe oranguru or two for draw support
- Alter of the Moon - maybe, depending if you use fewer than 3 float stones. Malamar can get retreat energy back.
3) other thoughts:
- Lunala GX is ok, but that stage 2 is slow and can gum up the deck, and when included in a deck with Malamar, is rather redundant. Malamar gets KO's by the wind, but only gives up one prize, and is much faster.
- over two turns, Lunala prism is worthless for energy recovery when there are two Malamars on the bench
- you don't need "as much energy on him as possible" and this can be hard to accomplish. Just get 3 energy + a CB/FFB and he can go on a run. Besides, Lele and Gardevore will benefit from 4+ energy on Mewtwo GX.