You're so right about the good outweighing the bad in the comic. I think a lot of people have trouble critiquing it because it's very long & hard to understand, and the people who put in the time to understand it obviously aren't going to hate it, so they won't give that much critique. & that so much of what people dislike about it is subjective. For example, I think homestuck is convoluted & hussie often thinks he's making something clear but isn't. He points this flaw out himself in the books.
Yeah, on a first read a looooot can elude you and sometimes something pointed out briefly on this seemingly irrelevant conversation later parallels something much bigger- The grounds for foreshadowing and building the puzzle that is Homestuck is there, but you really need to invest some time or have people point stuff out if you want to get everything, and even then so much is open to interpretation by design.
Ultimately, though, the message Homestuck sends is one of acceptance, of fighting back against an unfair World, of living and growing up and being yourself, so at its core its very message of optimism clashes against criticism- It’s hard to really hate something that’s trying to deliver a message like that, even if there’s a few miss-steps or things you dislike about the presentation itself.