The main reason many people dislike Clyde is that his negative quirks are played to a level of idiocy. Like how many times do we have to see him fawning over Lori or him liking baby shit or him relying on "Dr. Lopez"? Another factor is even with his positive traits, it doesn't make him stand out as a character. I mean, he's not a dick but if you're going to have a show where the main characters radically stand out, you need to do the same with secondary characters. Lastly, his role is not fleshed out good. Clyde's role is the male friend who's an only child. But they rarely flesh this out well. It doesn't help that's he is used for diversity points."Look at this black nerd with gay parents. HOW PROGRESSIVE". Yeah people exaggerate his dis likability factor and the hate he gets can get retarded but this is the internet so deal with it.
IMO, if you want to improve Clyde here this. Tone down his negative quirks or end them. Make him go through an event that gives him new perspective and develops him as a character for the better. Like he realizes him bagging Lori is impossible but Lori helps him with girls or he went through an embarrassing moment but strives to improve or he finds the courage to go through something he didn't want to do. Make stand out better. Being chocolate Lincoln isn't going to cut it. Have a scenario where he and Lincoln are radically at odds with something. Lastly flesh out his role in the show in a way that is understandable and enjoyable/admirable. Sidekick characters are usually written bad but if they can pull it off with Youhei from CLANNAD, anything can happen