I'm sure you'll find the answer if you go back many pages, but to save you time... IIRC, these are the main complaints:
First and foremost, unlike all his other works, Negima! did not have what you would call a true ending- there were literally dozens of plotlines left open, something that KA was known to in general never let happen. Then after that, since we all knew that Chao was a descendant, she also revealed that she was a descendant from an alternative timeline. Few authors can handle time travel very well, and in the end, KA showed he is also one of those who can't handle it well... basically a way to dodge the question of who negi ends up with in the end
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