Hi !
This might seem like a non-issue, because when you have that kind of problem, that means your game is going pretty well. And it is. So here to my GM "first world problem":
I have a player who like comics very much. His character is literally Doctor Doom, the mad scientist, villain and mastermind Victor von Doom.

When my player originally came up with his concept, he provided with a very decent amount of reasons backing his choice, including the idea that Darth Vader was, among other things, inspired by Jack Kirby's Doctor Doom and other pulp villains like Darkseid (http://en.wikipedia.org/wiki/Jack_Kirby, http://www.salon.com/2002/04/10/lucas_5/, http://ralphriver.blogspot.ca/2005/04/george-lucas-and-doctor-doom.html). I therefore agreed to let him play a very "doomesque" Star Wars adaptation of Doom, and he picked a Career and Specializations to match several aspects of the character, including Arkanian for species. We discussed at length several key aspects of what I would allow or not, and I tried to lower his expectations of "world domination". Using Force and Destiny's Sage and Niman Disciple, but also Scientist and Scholar (in which he invested most of his points). The end result is a very interesting, and not at all overpowered, character build. It's largely a fluff/concept character, not a powerhouse. Most of his XP went in Knowledge skills, Mechanics, Medicine and Computer (this last one at 5!). He has a power armor and lots of gadgets, but that's the easy part to manage.
The problem therefore is not mechanical, it's thematic.
I'm having a hard time reconciling both the mad scientist tropes of applied phlebotinum / handwavium pseudo-science (http://tvtropes.org/pmwiki/pmwiki.php/Main/AppliedPhlebotinum?from=Main.Handwavium), lightning fast "research", ridiculously fast invention crafting, gadgeteer genius tropes (http://tvtropes.org/pmwiki/pmwiki.php/Main/GadgeteerGenius), mcgyvering everything out of thin air (or plot) (http://tvtropes.org/pmwiki/pmwiki.php/Main/MacGyvering) .... with Star Wars's relatively "Space Age Stasis" science (http://tvtropes.org/pmwiki/pmwiki.php/Main/SpaceAgeStasis), fantasy outlook ( not hard Sci-Fi at all). I don't think it's all incompatible at all, it's just a matter of focus and PC vs. NPC thing. I mean look at the huge handwave material behind hyperdrives and lightsabers tech, over-the-top Rakatan Star Forge, science-defying sith alchemy, etc. It's just that in the comics these things can be constructed quickly, with no thought given to cost or impact on the world. It gets hard to balance the cost and time for players, and have the mad scientist do his thing, especially if contrary to comics, you known they are going to try to use these devices at every occasion (http://tvtropes.org/pmwiki/pmwiki.php/Main/ReedRichardsIsUseless).
What do you do when a PC constantly discusses the science of Star Wars, asks the cost of Cloning Facilities, designs droid "A.I." that he somehow wants to keep in his datapads, wants to build "organ printers", researches alien genetics to create hybrids, wants to clone and genecraft Force-users, and have an army of Doombots? I see the myriad story opportunities, but imagine how this must be when 3-4 times per session you have to manage the new science project the player brings up, which of course is totally different from the previous one and absolutely expensive beyond measures...
I am also having difficulty managing the player's expectations of playing a "villain protagonist" (even if his villainy lies more in master plans and clever ploys than slaughter, destruction and mayhem). The player is the embodiment of the forever-GM-person. He rarely gets to play. He is used to being the guy designing the NPCs, and he has a hard time thinking of himself as a anti-heroic/anti-villain protagonist. He dislikes the reactivity of heroes, the fact they do not try to fix the problems before they crop up. He wants his character to change the status quo, with... Doom at the top. But this often gets in the way of the group going on, you know, adventures.
So far I've tried responding positively to this by being fair to him. He is (obviously) a Dark Side Force User, with morality in the low 20's. He purchased almost all the cool Talents that fuel his concept. Utility Belt for constant gadgets (Scientist), Stroke of Genius (Scientist & Scholar), Careful Planning (Scientist), Valuable Facts (Sage), etc. He is the biggest Destiny point user at the table, and he is very, very proactive in adding to the story, despite him thinking of his PC as a somewhat mad mastermind behind it.
Lastly, I am also having a lot of trouble pitting this UTTERLY FEARLESS character archetype against any NPC with attitude, since by definition (and the comics back that up wonderfully) Doctor Doom does not accept being inferior to anyone, and challenges anything. Including Galactus, the Beyonder (see Secret Wars, http://www.comicvine.com/beyonder/4005-10300/) and basically anyone. Core to Doom's personality, he has epic Willpower (reflected in the character's Discipline and Willpower scores), just read about Doom (http://whatculture.com/comics/5-reasons-why-doctor-doom-is-the-best-villain-ever.php/2) to see how that might might sometimes be a problem... including Doom's arrogance and stubbornness...
Last game, we started Beyond the Rim, the group went to The Wheel and the player tried to hack Master-Com once he got to his hotel chamber. I allowed him to try, and a very RED dice pool was thrown, and he failed with despair. One of Master-Com bodies visited him to discuss this, but the player refused to bow down and apologize to the master of the station and soon he began fearlessly walking down The Wheel in search of the Master Computer Server (for research!), disregarding his security, and after a longish firefight (non-lethal from start to finish) he was arrested. Since his character is fearless, he shows no sign of redemption, and Master-Com, who is being bribed into releasing him, has a hard time letting this madman rampage the session once more.
What can I do to turn this GM challenge into a fun experience for the player without cheapening the other PC's experience? Up to now they have been relatively OKish with the idea Doom would think of them as "minions" in his delusion, but the imprisonment "for science!" was kind of the cherry on the Sunday.
Help!
Edited by BarbeChenue