you know the thing about the "best ending" is that while bittersweet, it truly is the best outcome i could think of.
from what i know the game starts long after the real fio and crow could be saved. you may not be real, fio may not be real, but you still feel the memories, the love you had for him. even though you aren't really crow (and supposedly don't have as much capacity for remorse as an original (i wonder what other things the clone doesn't have that the original does)) you still care enough for fio to be willing to sacrifice your life for what is left of him.
even if you and your love are fakes, you still have eachother, and that's enough for you two to be happy. you may be an imperfect clone with a bullet in his shoulder who is on the run from the government, but at least you have your imperfect clone twink boyfriend, and that is all you need to be happy.
i'm glad i got the best ending.