My pleasure, is always interesting to see something from a different perspective, it help me to see with a more objective eye the story, so I thank you.
And true all of you said happen, but at the same time he confront Lilith by himself before and after, on the train Aiko stall Moloch but when he's pulling the gun trigger ( and we don't know if Aiko could have been so fast to avoid the shot) he block Moloch with the spray, for the scene with Azazel I agree with you (but I don't see it as a weakness show, instead that was a turning point for him to understand how deadly serious was the story, since that moment they all got out from the danger almost unscathed, that was the real confrontation with the danger they are facing, infact if you make the wrong decision in that scene before Aiko appear, that's a game over), and this is shown when he kill Asmodeus to free him from Astaroth's mind control, a weak character could never have the strength to kill him, at least in my opinion.
I would say that he grown strong mentally and physically in a credible and gradual way during the play, instead of seeming endowed with preternatural abilities as often happens in other games, and which while in an adult person this would be an acceptable thing, in a teenager I find frankly not very believable, this is again my personal opinion.
The scene with the thugs is the only one that leaved me puzzled I'm honest, but I think Caribdis wanted it that way to give Mike the catch lights so to speak, a well deserved one solo moment, since Mike is so cool that is able to steal our attention from the MC, whit his great personality.
But I don't want to drag the discussion too much, i just hope you will appreciate the MC a little more after finishing the game I hope, if not, well at least there's a ton of good things in the game regardless.