Both quarterbacks have been at the top of their game in 2014. While Andrew Luck certainly has more career ahead of him, it would be hard to take Luck or any other quarterback over Brady right now. Luck has been more turnover prone (although to his credit he has also thrown more passes). Brady has been more accurate and mistake free, but Luck has thrown the deep ball better (despite Brady's recent resurgence). Brady has better pocket awareness, and his intermediate throws have more zip on them, thanks to his signature tight spiral. Overall, you have to prefer Brady's command over the offense, pre-snap reads, etc.
While Brady has all of the intangibles that you look for in a quarterback (and that's not meant as a slight to Luck, who's well on his way), there's one thing he doesn't possess that Andrew Luck does: athleticism (and how to use that athleticism).
RIchard Hill made a good point earlier in the week on Tom Brady's improved mobility. He's right. Brady is moving very well in the pocket right now, but he is obviously still not much of a threat on his feet. Andrew Luck is. Consider comments made by Patriots head coach Bill Belichick earlier this week:
"He's like a sixth receiver in those situations. You have to cover the five eligible guys, but you also have to keep an eye on him running for three, four, five, six yards something like that where it's not that far. He can easily get that. It puts more pressure on the defense to take away that sixth option."
Overall, according to ProFootballFocus.com, Andrew Luck is 8th highest in the league in time to attempting a throw. He leads the league in attempts coming 2.6 seconds or longer after snap, showing his ability to create after a play breaks down. On those throws, he's completing 59.1% of his passes, and a has a QB rating over 91.6. Brady's numbers are technically better, but his percentage of throws with extra time are second lowest in the league.
If you added Luck's ability to make plays on the run to Brady's overall skillset, you would have the greatest quarterback that ever lived. Although Brady might already own that title... and although a long way off, perhaps Andrew Luck is headed down that path as well.
So, what skill of Luck's are you giving to Tom Brady? Is it his athleticism? His deep ball? Something else?