I think the thing that hurts this movie the most is its attempt at a "clever" story structure. Movie opens with a hint at great climax of the story... we then flash back further to 'earlier that day' where Kronk receives an urgent llama-gram from his Papi... this results in him recounting two other flashbacks... before returning to the first flashback... before leading us to the climax.
You follow all that? I'll admit, I barely did and I enjoy movies like Memento.
Also worth noting is that the opening song. While upbeat and bouncy, it is totally useless in its goal of establishing the movie's overall theme. I mean, compare Tom Jones singing "Perfect World" in the original New Groove with lyrics like 'he was born and raised to rule, no one has ever been this cool'. The song clearly tells you about who Kuzco is--or at least, who he thinks he is. Compare that to poor Kronk's song... I have no idea what that woman is saying! I actually turned on the subtitles at one point just to try and figure it out... okay, I get it, 'true to your groove'. If you're going to have a song that's stating the mission statement of the movie, at the very least make sure I can understand what it's about!
And yes, Kronk, while a loveable sidekick was really stretched here to carry the entire movie on his own. We loved him in the original New Groove because his total innocence was a wonderful counterpoint to Yzma's manical objectives. On his own though, Kronk just doesn't pack the same punch.
The entire 'true to your groove' theme was perfectly addressed in Kronk's portion of the epilogue of the original movie. Unfortunately, Kronk's New Groove takes that small catchy moment, throws in ten times more complexity than is really necessary, to ultimately get us right back where we originally started from. If there was ever a definition of a largely pointless exercise, that would be mine.