It's funny how different people perceive things. I liked the cheeky ninja uke from the start. I guess the intrepid young love interest is a type of trope, but you don't often see ballsy ukes in yaoi. The rape is standard yaoi, though I thought the play was imaginative and the old school film use was a nice touch. But even in the first chapter, I thought there was something a little different--both about how Aki wasn't a pathetic victim even if he was raped, and in the end when Asami sympathizes with Aki and places an hand on Aki's head. I am not saying it's a huge departure from any romance novel you may read, but there is something there.
I also think that the balance of romance and drama in the currant arc really works for me. The central question of Aki's struggle against accepting his feelings for Asami and Aki's fear that giving in to love will change who he is still drives much of Aki's actions. Sure the plot with Sudou and whomever else matters--but it goes hand in hand with the romance.
I agree with most of what you said, except the "not being a pathetic victim" in this manga at times came across as the rape being glanced over or treated too lightly, at least in my eyes. Which kind of is another trope, in a way. What really made it unique to me was the Hong Kong arc though, because it's pretty rare to have the main couple actually separated for such a long time, so that really stood out to me. But I like the way their feelings seem to develop at the moment as well. I just hope they'll continue to make progress.
Did you guyes see that from yamane's twitter?
https://scontent-cdg2-1.xx.fbcdn.net/hphotos-xaf1/v/t1.0-9/12373418_560816820750198_7471867819005839216_n.jpg?oh=3800e38c1defc3e123adaecfff2a112c&oe=56E697E8