I liked CotM for the most part. I don't think it's aged well at all, though. :\
The level design was kind of iffy for me. Some places, like the Machine Tower and Observation Tower, were excellent. Several places, though, had really awful level design. Like CoD-worthy. The Abyss Stairway, Eternal Corridor, and Audience Room come to mind.
I was also wasn't all that hot for the animal-versions of Rondo's enemies. And the DSS card system was really crappily implemented. Grinding is never fun; making it to where you have no idea what enemies you need to kill over and over just makes it hellishly bad.
It's an alright game, but I prefer all the other Metroidvanias. But I still like it.