I love Kingdom Hearts, but I can think of several reasons.
1. The fanbase. Oh god the fanbase. 2. The fanservice, mainly in the forms of Final Fantsy VII and VIII. 3. The story is as convoluted as ****. 4. It's a JRPG, which means it's automatically bad in the eyes of dudebros. 5. It's a crossover with Disney, and Disney is for "teh kiddies".
Those are the big ones.
My sig will never happen, but it would be awesome if it did.
Biggest complaints I've seen are relating to the lack of a KH3 and the saturation of titles over multiple platforms. People don't like having to play handhelds in order to get the full story on a series that started on consoles. Others immediately write off all the handheld titles as terrible/milking of the franchise, but those people are idiots, so best not to mind them. The lack of a focused platform is a valid complaint though, even if it's never bothered me personally.
Besides that, KH's story is arguably more of a convoluted mess than MGS's, which also bothers some people. Again not me but I can see where it's coming from.