Strong agree on everything. I just binge-watched all six seasons, but I can't remember if Rusty was still under protection by season 3, or if Sharon had decided that he was no longer under immediate threat.
The Rusty/Gus relationship was always uneven. Had they been good friends, sure, I might have bought that. But I don't know if it was the actor's chemistry or what, but the two barely seemed to tolerate each other at times. Something I noticed from the last few episodes that made me uncomfortable...Gus needs protection from Stroh, too, since Stroh was a customer in his restaurant. So he moved in with Flynn and Rusty and pressured Rusty to let him sleep in his bedroom. He even got Andy's approval. If we were watching a show with a male character pressuring a female character to let him sleep in her bedroom, well, that would be the beginning of a Major Crimes episode. But it's ok because they used to date? And are the same gender? Nope, not to me.
The rest of the squad is great and could have been utilized more. I didn't mind Nolan being brought in, but disliked Cami.