One flaw I'm glad they gave Spencer, and also the thing I see him criticized for is his emotional immaturity. But I'm glad he is, because it just makes so much sense.
I'm speaking from experience here, as an adult who raised herself as a child. But when you raise yourself, you have no one to show you how to be.
Spencer's dad left him a pivotal time in his childhood and his mother was schizophrenic. It was him against the world. There was no one to teach him how deal with his emotions in a healthy way. So as an adult, we see him lash out when he holds his emotions in, and we see him being petty because he doesn't know how else to deal with those feelings.
And when you combine that with the horrific bullying (also speaking from experience), you see him making assumptions about the people he LOVES because the only experience he's ever had with people who were well liked in school was a negative.
Like when he assumes that Morgan was a jock because he's muscular, or when he assumes that JJ was a mean girl because she was blonde, popular, and from a small town.
We know he dealt with the football goal incident entirely by himself, so it makes sense that, to him, everyone would be split into 3 categories: the football team, harper hillman/alexa lisben, and the bullied kid (him).