Ive always found Cotton to be unique, not quite a serious shooter like gate of thunder, thunderforce etc, but not quite a cutemup, just compare it to the snes version of cotton.
cotton has more diversity in its back grounds, MC the level will look the same at the start of the level as it will at the end of the level, Cotton has larger sprites and far superior animation, cotton has some of the most beautiful hand drawn animated fx of its time, 2nd only to rondo on the system in my opinion, they both have the same amount of colors on the first level, just over 100.
Superior sound fx, CD quality music and cutscenes, on a tech level magical chase is not in the same league.
I do have a hard time choosing which one I like better as far as gameplay goes though, but with all the above mentioned I went with cotton.