Just thought I would recommend this manga to you if you haven't seen it already. It's still ongoing, and the latest work by the same author/artist as the excellent Skyhigh and Sidooh series. It's only just started (into the third volume), but it's really strong (both in writing and in art). Honestly, Kubo's a fascinating "villain."
I was curious because I was bored in a bookstore waiting for my TDKR showing and picked up an "Art of Hellboy" book. recognized the art in your avatar from the way he draws skulls. I read the introduction and he seems like a great guy, he cares a lot about what he's doing. His use of black is also pretty brilliant. I may have to give Hellboy a shot sometime.
I think you're dealing in absolutes too much about where these movies draw inspiration from. It was already noted by Webb that this series draws from both the 616 canon and the Ultimate one. Osborn isn't the only way to go.
The idea of a boy and his mecha really fascinate me, both east and western takes on such stories. I was thinking something along the lines of The Iron Giant meets Death Note: a boy comes across this robot he forms a mental connection with. The large, humanoid machine itself not sentient and the initial connection flooding the protagonist with a series of cryptic imagery that become relevant later. So he can control this machine with his mind, greater distances making it harder to do so.
The thing is, this mech is like a child: it learns through the experience gained by when its being controlled. When the connection is "turned off" (not really severed but more like muted), based on said experience, the robot becomes 'independant'. Eventually, the boy and it form a bond but like, imagine trying to do your homework/balancing highschool drama/not getting in trouble with the law when you're navigating this robot all the time or when you're at a dance and suddenly the robot's about to tango with godzilla or some shit