My opinion on the matter, coincidentally, is that if Chrono Cross had NOT been connected to CT in any way, I doubt it would have received as much of the flak from players that it did, for precisely this reason -- framing it as a CT "sequel" invited unfavorable comparison from the jump.
Fox HarperI'm in a similar place with Chrono Cross -- the game's systems are internally cohesive, and the game's structure works. But it exists in a cultural context where it was billed as a Chrono Trigger sequel and given how large CT looms in the genre space, I think it's reasonable to consider it!