That's a great observation about the mutually antagonistic relationship between audience and author. Maybe that's inevitable on some level, but it must have been particularly pronounced in Homestuck, given the vague barriers of interaction that the internet and its diffuse methods of communication create. People might have been 'right' in the abstract about a character having more potential than the narrative was giving them,, but those critiques must have inevitably been perceived--maybe not unwarrantedly--as grating demands to an author who is in close direct contact with audience opinion.

What I will say about Equius is that being a "joke" never stopped anyone from being an excellent, interesting character. I don't have a high opinion of the guy myself, but his contradictions and what he represents about Alternian society are certainly interesting and make him interesting to read. Plus, you know. It's funny. The joke about him does not stop from keep being funny.