When a player starts making it clear that he disapproves of your view of how a game should be run, and consistently disapproves of the system you've chosen... It can get really grating. "Well, how would this work?" "Well, that's not something the system supports, but it would be approximated with that. The effect would be to knock them out of the combat for one round."
Yes, it's not the perfect system. The point isn't to make any story you can imagine. It's to take a common ruleset that everything works under, and create a story that treats everyone fairly by the same rules, and set some forces at odds with each other, and see what comes out. You know what you're capable of because the rules tell you. You pick and choose your fights, and you have some basic idea of what kind of chance of success you have before you choose an action. Trip, grapple, attack, defense, all of these combat options were created with an essential balance in mind. If one side has overpowering "stunt" type abilities, the other needs them too, and then the math of the situation starts spinning wildly out of control. The greater the variation, the more unpredictability comes, and the less anyone is able to play the game effectively.
The reason a katana does 2d6 damage and takes the Exotic Weapon Proficiency feat to use is so that when someone comes on screen with a katana in hand, you *know* that person is a badass. A katana that does d8 and can be simply used with Archaic Weapon Proficiency is just a sword. When you say "I grab his forearms as he comes at me and yank downards so as to better boot him in the jimmies" it has to translate into game terms, or else you've just got a free-for-all "No! I shot you first!" going on... And I think this system has done a better job of giving players that chance than any other has for quite some time.
If the players are significantly more powerful than the baddies, the game becomes a one-sided storytelling session. You need that balance to have real risk, and you need real risk to feel a real reward.
I think when it comes down to it, all the complaints come down to one thing: he doesn't trust me as a GM to make the game interesting to all the players; he thinks he'll have the moment when he shines, and then be sitting around twiddling his thumbs the rest of the time. Annoying. The most important thing a GM must do is balance spotlight between players, followed closely by keeping the lights on the rest of the stage all the time. You can't just have a one-player scene last very long at all, or else you lose the other players.
(Edit: oh, and finally got a d20 modern lj icon)
Further edit: Hmm... it occurs to me that since I'm learning about this here game mastering thing, he may not have good reason to trust me as a GM. I've even said things like "I hope I do this well" and stuff... So where does that leave me?