Glee has huge issues. Single biggest character issue is Sue. One of the biggest mistakes the writers made was Making Sue's behavior's larger and larger. Lynch is absolutely wasted in the ole as its no longer funny in any real way.
2nd is Will, when the show started we got to see much more coverage on the adult storyline that was centered on the character of Will. But by the half point of the 1st season it was dropped, and then focused solely on Emma, Sue and the students. The character has always had issues (why do you think he stayed with Terri for so long). But now to show that side of his character its getting to the school and not just with Sue or Emma but his actions with his students (this is fairly new) and is massively harmful for the character. An episode here or there OK, I can understand, but that behavior can't remain with the students. Part of me wishes to see him and Emma and Sue completely removed from the show.
Two many characters. The show has tried to have its cake and eat it too. Clearly the show is going to feature Rachel, Kurt, Finn, probably Santana until its end. They remain (with a couple of other exceptions) the stars of the show. But the show didn't just include those characters this year, they also tried to include every single cast member who graduated last fall. That was a huge, huge mistake.
And while I have liked a couple of episodes that have focused on the new students, I still over all prefer the New York characters.
They really need to cut the dead weight on this cast. Actress who played Brittany is pregnant, so I am hoping they drop her character (really, really wish this as I think for the most part Brittany is a one note joke that stopped being funny in season two).
It appears that the show is now setting up three locations for stories. New York, Lima High and the university of Lima.
All I can say is they better really focus on characters, because with this large of cast it does no good for anyone.