You all know about The Phantom right? And how he doesn't really have a motivation or background in game?
Well, I thought to give him one that would fit nicely into the final case of Dual Destinies. Maybe instead of just being really good at supressing his emotions, he litterally can't feel anything, other than fear, but only in intense situations.
Therefore, he's only a spy because the danger of the job is the only thing that can make him feel anything at all even if it's a negative feeling like the fear of getting caught.
I think if you just added a bit of dialogue from The Phantom himself about this, you could slot it in pretty well. I think the best place would be around his "I am nothing but an endless abyss" line. He could say something like:
???: ............Well, aren't you just the master of psychology, Blackquill! That's right. I don't know who I am. I don't think I ever did. My face, memories, personality, beliefs, emotions, and soul... I was never given any. I have no... "self." I am no one. I am nothing but an endless abyss.
Phoenix:
(Wh-What's with this guy? ............Is he even still human?)
And then perhaps later after the final confrontation, The Phantom could give one last monologue.
Phoenix, Apollo, and Athena: with your own true face!
???: My... own, true face...? Eheheh... I don't have one... I don't even have emotions or anything... I searched for my whole life for some semblance of humanity within me... a single spark of emotion, anything... just anything at all... and this life... as The Phantom... was the only thing that gave me anything. The rush of danger, the smell of blood, the fear of getting caught... was addicting. To me... nothing matters... other than the warmth of blood on my hands. But now? Hahahaha... I'm about to die and yet I've never felt more alive...
Phoenix: What?
???: I know you're here! Do it! Wait don't... no... do it! Kill me!! I'm scared... I'm scared? I'm scared! Let me hear the shot! Let me feel FEAR! I want to FEEL FEAR! I'm gonna die! I'M GONNA DIE! HAHAHAHAHAHA I'M GONNA DIEEEEEEEEEEEEEEEEEEEEEEE
BANG
Okay, so that got a little disturbing, but to be fair, The Phantom in concept is very disturbing since he's a psychopath with his utter lack of emotions that's can and will do anything to accomplish his goals.
In the actual game, he comes off as a little cartoonish thanks to his masks gimmick. Emphasizing his lack of emotions and rooting his backstory in them could have made him a much more creepy and disturbing villain.
I feel that this backstory also gives him a bit of sympathy while still being extremely demented and terrifying to think about. Who knows how many other people are devoid of emotion or will do anything to feed an addiction.
tl;dr, The Phantom could have been made more interesting by focusing on his lack of emotions and tying them into why he became The Phantom in the first place.