I think Kou, in the end, chose Ao because of the nine years that he helped and also as a form of retribution for all the times he betrayed Ao.
See, the relationship between Mikuni and Kou should not have been too long (I suppose) after Mikuni believed what everyone was saying and did not seek the truth. If Mikuni really loved Kou, he would have run after him.
I get it, but I think it would have been better if Kou chose Ao, because he loved him, not because of his sense of guilt (their whole relationship was based on that). And I realize they've been together for a long time (while his relationship with Mikuni was brief). That's why I said it's more realistic that way.
We don't know (as far as I remember) if it was possible for Mikuni to find out the truth.
In the end, I believe that Kou loved both of them, but in different ways. His relationship with Ao was steady, but he was extremely attracted to Mikuni who was his type. I realize though that in real life one wouldn't end up with their first love (or even their "type" ;p), but still... Yaoi is always an idealized version of reality, that's why I'm complaining about the story ╮(￣▽￣)╭
Personally, I'm a bit dissapointed, but I don't hate the ending. It feels more realistic after all.
What bothers me is the fact that Kou doesn't seem to be angry after realizing Ao was hiding the truth all that time. I'd be furious. After his memory loss he was helpless, like a newborn child and he trusted Ao the most (not only his lover but more importantly his childhood friend!). That was wrong. I can't even imagine how Ao could live with that burden, fearing Kou would find out the truth and eventually reject him.
Kou was even worse, cheating all the time, promising this would never happen again... I don't think he really loved Ao, who was just convenient for him. He even admits he loves Mikuni. After all Ao deserved better.
Well, as I said, it feels more realistic though. It's a good story, not all lovey-dovey. I kinda hoped Kou would end up with Mikuni, but well...