Aigis is indeed the best character in the damn game, and Akihiko is the best male character even though he is the very definition of the 'When all you got is a Hammer' trope in terms of his drive and development, I felt he was sort of static which is not a bad thing. Though I do regard the female route as needless and pure fanfiction I do think we see a lot more of why Akihiko is who he is in his social link route than the male route.
Ken I can understand, the poor kid has been through hell and no one would ever believe him, not to mention with the trauma he's been through can you honestly blame the kid for doing for what he was going to do even if it was utterly wrong, especially when I believe that revenge doesn't solve anything?
Fukka is very developed in my opinion since she goes from being very passive and timid to very courageous and I would even say she's the anti Ken, despite the crap Natsuki did she protected her and they became best friends.
Koromaru is an expy of the dog Hachiko, which I fine very heart warming and I like her very much.
And Shinji, just my god Shinji, he's basically like Wilypocalyse PB but with Zeta's attitude problem before she became Sakura's friend and her deep down protective nature.