One very interesting thing about this show was the protagonist (Shuichi Kagaya) wasn't really the main character in its core plot. In fact, it was the antagonist (Kaito) who seemed to have played that part in the beginning.
Don't get me wrong though, Shuichi was the MC in the ongoing story. Speaking of him, he certainly doesn't look strong enough, even on his monster form. I mean, a mascot with a gun -- and that's it.
But if we consider his unique ability, then yes, him looking weak was a necessity. As he could look absolutely frightening, when merged with another monster:
Shuichi and Chihiro Yoshioka after metamorphosis
Though, it's Clair Aoki who merges with him most of the time. And sadly, I don't think they are strong enough compared to the other 'rares.'
The only way I can think of, for Clair to fully use Shuichi's potential, was for her to ask Alien to turn her into a monster as well.
And regarding Alien, he reminds me of Kyuubey from Puella Magi Madoka Magica. Both grant wishes, without taking any precautions.
Now to the side characters... I like that there's an out lesbian here, and she even has a role of a leader.
Sayaka Koyanagi with Miku Aihara
Meanwhile, Subaru reminds me of Sasori, the puppet user from Akatsuki in Naruto Shippuuden. They both have 'parents' that guard and attack for them.