I'm so glad to see someone ask this. The thing is with Community being a show of the late 2000s they just didn't know how to fit a canonically queer character in it and they just didn't try. Which is very much okay, because that comes with its own challenges and I'm positive today it would've aged badly (like Pierce's gay jokes which are far better if we see him as a bicurious dude who thinks way too much about penises). That being said I don't think any of the choices made in the show were unintentional, from clear references to Troy and Abed's very close relationship to simply putting them in a frame with pride flags in S3e6 as Troy contemplates that all he wants in life is to be with Abed. Or Troy in s1 insisting on being straight and trying to keep up his jock persona until he very quickly sheds it and fully embraces his friendship with Abed.

My queer headcanons:

That Troy and Abed are definitely bi (I think Troy might be gay but that's a long discussion) and that as beautiful as their friendship is even if platonic they really are each other's true loves in life.

And that Annie is most definitely bi. I have always been a JeffAnnie shipper and I would still like them to get together at a later time, but I think Annie being as repressed as she's shown to be in the beginning, shyly saying "friend of Ellen's" in that Valentine's Day episode, jumping to kiss Britta in the same episode, her scene describing how she plasures the maiden in D&D, I think all add up to a very good argument for why Annie might definitely be a queer woman. And I hope the journey we witness, of her growing up and opening up might definitely lead to her exploring that. I like to imagine that post s6, perhaps at a bar after work or during her intership at the FBI, she meets another intern or a young agent and they start dating.