Mega Malamar elevates it's base form's design by going all in on the 'supervillain' trope, giving him an elongated body and a fresh hairdo. By itself, it stands out like a freak in a good way.
Then you fall down the rabbit-hole of it's design origin. The long frills along the side of it's head resemble shoulder-pads, reminiscent of comicbook villains such as Mr Sinister and Annihilus. It's hairdo resembles a massive head/brain, which it is able to stimulate using toxin's from it's tentacles to grow stronger, similar to characters such as Bane who injects substances into himself to grow larger musclemass. And did I forget that it's body was shaped like a big M? Overall, Mega Malamar highly resembles Mojo Jojo if he was a squid instead of a monkey.
Not to mention, the bioluminescent lights that glow from both the tips of Malamar's tentacles and thin body both serve distinct purposes in it's design. The rainbow lights are evocative of deep sea creatures, which the original Malamar was based on (the giant squid), and these rainbow lights can be seen in comb jellies. As for the Green and Purple rings that sway in hypnotic rhythm, green and purple are colours often associated with super-villains (see Green Goblin, Annihilus, Joker, most of Lex Luthor's armours, and even depictions of Skeletor from He-man). The glowing spots a clever way to elevate an otherwise hit-or-miss design.
Mega Malamar definitely deserves more appreciation, and it was sad that it's hype died down after the release of it's ability.