You nailed it...he's either FBI/CIA/Black ops. The government/powers are trying to coop his powers/knowledge/inventions for their own selfish reasons. Either by observation, experiment or coercion presumably. He's sort of a prisoner on earth. I wrote a post on the parallels to Howard Hughes, who was either held captive or went crazy living in a Vegas hotel (see the aviator) so his wealth could be pillaged. The cover story is that he went crazy, but he could have been forcefully strung out on drugs to cooperate and hand over his wealth and knowledge. He was also harassed through the judicial system and the red scare.
Similarly Thomas is fed alcohol in an attempt to break him down. His friends, and employees sell him out. Bryce betrayed him and married Mary Lou and kept them apart. His limo driver went to work for the enemy and held him captive. Mary Lou was compromised and bought. And so on.
You can also draw a parallel to Nikola tesla, who's patents were confiscated after he died.
I'm still not sure if he's indeed from another planet or just a time traveler.
There are also some hints about the destructive/limitive powers of capitalism within the movie. The black general talks about how they have to slow down technological advancement to try and preserve American society, hinting that any advancements that happen too fast might destroy all those profits (say, free energy, free music, or use your imagination) and status quo (power structure). This brings me back to Thomas' interest in "transference of Energy". A very interesting thing. Also references Tesla and wanting to transmit electricity over the air (see also The Prestige...also Bowie Played Tesla), but assholes like Thomas Edison and JP Morgan wouldn't allow that, because it wouldn't make them rich and powerful. If government was really about the people, they would use tax dollars to build infrastructure that could provide free energy, free internet, clean free water, etc.