How would Nihilego even work?
...Nihelego? You mean with Lusamine inside it? I really can't see this being an Echo, so I voted Shadow Mewtwo.
I think this one's coming from me. Mostly I was trying to think of a Pokemon who would 1) Be likely to make it in, 2) Had a vague body shape that maybe could be placed on top of Mewtwo, and 3) Maybe had some kind of energy attack? Was I grasping when I suggested it? Yes. Do I know that much about Nihilego? No. Do I like the design of Nihilego and think it'd make an interesting addition to Smash? Yes!
In fact... It's Moveset time!
So with most of the grabs, arials, tilts, etc. most of Mewtwo's moves can still be used, just instead of the moves being "infused with dark energy", they'd be infused with poison. Dark energy is purple, poison is purple, they're practically the same thing!
Let's look into the specials:
Neutral Special*: Mewtwo's is Shadow Ball, I'm going to say Nihilego's would be Power Gem. Charge it up, fire off a beam of gem light. Similar enough, if not to Mewtwo's then definitely to plenty of other characters.
Side Special: Mewtwo's is Confusion, Nihilego's could be one of a few. First, Psywave. It'd function similarly by using a psychic attack to lift opponents of act as a shield. If we want to go a bit outside of Mewtwo's confusion animation but would still act in a similar fashion: Constrict or TIckle, Nihilego would use it's tentacles instead of psychic energy to toss fighter around or stop incoming projectiles.
Up Special: Mewtwo's is Teleport. Nihilego could perhaps use Substitute? They're able to learn it through TM so... OK Nihilego doesn't have a good stand in for Teleport, so let's look at some other Up Specials we could take and use (Chrom takes moves from multiple sources, so it's possible for echoes). Let's take... Greninja's Hydro Pump? Instead of shooting out spurts of water, though, Nihilego would use Acid Spray and shoot out spurts of Purple acid. It would function nearly identically, only have a purple re-skin.
Down Special: Mewtwo has Disable. In terms of having a similar in-Pokemon move that could work, Nihilego doesn't have one. However, looking at how Disable works in Smash, Nihilego could use Toxic Spikes. Nihilego's lobe would glow slightly purple and a nearby fighter would be knocked back and surrounded briefly in purple, denoting a toxic spike having been fired at them.
*Other idea for a Neutral special. Again, see the note on Chrom, one echo can take moves accross characters. Nihilego is known for absorbing lifeforms- for taking their power after eating them- almost like... Kirby? What if Nihilego's Neutral special was a re-brand of Kirby's inhale? Nihilego would grab a fighter, absorb them briefly into it's lobe, and would take their Neutral and maybe even have a type of "hat" floating inside of it.
For the Final Smash, there's no way around it we'd have to use either Beast Boost or Venom Drench. However, thanks to Dark Pit we know that echoes can not only have different final smashes, but completely unique final smashes. Beast Boost is the clear choice, however I'm not sure how it'd translate into Smash. Probably surround Nihilego with an aura and have it zoom around onstage, Pikachu like. It's not really what Beast Boost does, but it... sort of works? More translatable is Venom Drench, where Nihilego would spew a bunch of acid and poison on an opponent dealing massive damage.
Is it a perfect echo? No. Is this what Nihilego fans would want? Probably not. But, the echo could exist, it's an option for people to vote on, and we'd get a cool alien jellyfish as a fighter. I count that as a win!