I actually find it amusing, especially since I've been in other fandoms, how seriously people in the QaF fandom take their ships. I mean I remember back when QaF was still airing (during the hiatus between season 4 and 5 was particularly bad) the epic ship wars that occured. In fact I created a group over on LJ, where people could discuss various ships *without* flame wars occuring, just because things were getting so crazy.
I'm so glad I wasn't around when the show was still airing, because seriously? I'd have had an aneurysm. I would have. Totally.
See, I've never felt this way about a TV show before, and I've never "shipped" a couple, and based on how you're using the term, I'm not sure I DO "ship" this couple. It sounds to me like you're saying it's, like, a pairing you're rooting for, but to me, Brian and Justin are true love, soulmates, destiny and not just a favorite pairing that I might change tomorrow for some other couple on another show, or even another couple on THIS show.
I will never feel this way about another show, and I have no interest in watching another show this way again, and don't want to ever feel this way again.
As to Brian and Michael having "chemistry," I felt that there were moments when Michael's very intense attraction to Brian was met by him with a kind of abstract welcome, or fanned by him into bigger flames out of his own need (301), and times when you could see Brian's need to be loved and feel safe lead him into playing with Michael in ways that crossed a line (after Michael's father's funeral), but never once did they have what I'd really call anything more than just garden-variety TV show "we're supposed to be attracted to each other now" chemistry.
But Brian and Justin melted the screen every time they shared a frame. I've personally never seen anything like in my life. I really have no clue how anyone can dislike them, or either of them, or see them with anyone else. It's genuinely bewildering to me.
Of course I realize that there are people who hate the music I love, who don't like dogs, and who wear ugly shoes. I get that I don't rule the universe. I'm just trying to express the enormity -- and singularity -- of my obsession with Brian and Justin.