Thats what you call an epic "plot twist"
I absolutely loved it.
YEAH me too ε=ε=(ノ≧∇≦)ノ
I think you hit the nail on the head with your two plots description. It seems like the author tried to redeem Shinya in the latter half of the manga by making him into a cute, pitiful character but, in doing so, she pretty much threw Yoshito under the bus and just sort of shuffled the story line. Rather than a plot "twist", it was more like a plot change; like the author just changed her mind halfway through and tried (but didn't succeed) to make it make sense.
Well, I did enjoy the story, but definitely got mixed feelings about it. The beginning and the end almost seem to belong to two different plots. Yoshito's character was kind of cast aside later on, but it was supposedly a fight/misunderstanding between revolving around all three of them. That part didn't stay consistent. The pairing bothered me (as it did to many others). Shinya and Ryu's relationship is just plain odd. Love is not what I would use to describe it. It's pity and wishing for attention that was not received in the past. I think a plot around YoshitoXRyu and Shinya remaining the cruel antagonist would have been stronger. Still a good read, just...odd.