Wow, lookit, over here on IJ and about to wade in on a QAF discussion! \o/
Took me a few years and LOTS of discussions to change my mind about 513. The things you mentioned (some of them, at least) were my thoughts at the end, but later I came to see most of it in a different light.
Brian and Justin are still together. The story of QAF is a story of boys to men. While Justin is the emotional equivalent of any of the guys, he is also still a very young man. Brian, Michael, Ted and Emmett have grown up and made their way in the world, and at the end of 513, it's Justin's turn to do the same. He's going to see if he can make a living at his art, same as Brian did with Ryder/Vangard/Kinnetik, as Michael with Red Cape, Ted as Brian's CFO, and Emmett as a party planner. It's just that we see so much of Justin's growth from boy to man that when we get to 513, it seems as if he's all done. But he's not, he's just beginning.
As far as marriage goes, yeah, I wanted that. But then, much later, I realized they didn't need vows, as Justin said. Maybe later, down the road, once Justin is established and perhaps living back in Pittsburgh, they could take that step. But why would they get married, just to have Justin up and move? Justin was smart in deciding not to marry Brian. And from what we were shown, it was damned good for Brian, too. He started acting like a Borg, but we know why that was.
Contrary to popular belief, PTSD does not go away. It can be dealt with, with therapy and, at times, medication. But there will always be triggers. We saw it happen in 402 with Justin's reaction to Darren's bashing (Pink Posse) and again in 510 during the bombing (Brian calling out to Justin in a mirror to 122). Again, even though nothing is said, Brian finds Justin bleeding from the head, and to make matters worse, Michael is hut and Brian can't fix it. Luckily, Justin figures it out and stops the train before it wrecks.
As for Mel and Lindsay...don't get me started on why they DIDN'T have to leave the country. First off, it's 2005, and people can't just up and move to Canada the way they once did. You used to be able to drive across the border whenever you wanted, but not after 9/11. Plus, there's the fact that Mel would have to learn a completely different type of law to be able to practice there. We have constitutional law, they have provincial law...someone wade in here and help me on this! But yeah, still...plot hole the size of Jupiter.
The funny thing was that the one storyline that worked better than any of the others, that actually made the most sense, was Ted and Blake. By the time they meet again in 513, they've both grown, beat their addictions, and are ready for the relationship they started 5 years before, meeting as equals. I loved their reunion.