Hmm. I'm not sure if the Mag mod you're considering is an LED or an incandescent. I'll assume it's LED, since we're in the LED forum. I'm also unsure whether the Mag mod will be a Lux I, III or V. Finally, I hope you meant to say the Mag mod will be powered by AA cells, not AAA. I think the AAA cell is probably a lousy choice of battery for a host as large as a 2D. The mAh to volume ratio just doesn't cut it. Besides, it's not that difficult to fit eight AA cells in a 2D, especially if it's been triple bored.
Is runtime a critical consideration? Eight AA NiMH cells rated at 2500 mAh will hold about 24 watt hours of juice, while a single 18650 cell in the U2 will barely hold 9 watt hours. A fully loaded Mag 2D should run a long long time at output levels similar to a U2. Then again, it's going to take up a lot more space in your coat pocket.
There's a bunch of picky personal details to consider. If you really have a thing for the Mag's side mounted switch, that might be a consideration. The U2 has a tactical style tail mounted clicky. The U2 has a pocket clip, which could be good or bad. Some people hate the U2 clip. I seem to like mine. On the other hand, a pocket clip on a Mag 2D is just kinda silly.
I'm still firmly convinced that all U2 lights are bound to have some kind of donut. My first one had a moderately nasty donut, while the replacement they sent under RMA is only barely noticable. After you use it a while, you just kinda forget about it. If your Mag mod has a Lux V, it's bound to have a donut too. The switch on my original U2 tended to jam up, but the one on the replacement still feels mighty good. I think if you buy direct from Surefire, you're more likely to get a really good one. And, as many will tell you, a really good U2 is an impressive light.
All that said, if you can get a Surefire U2 for the same price as an LED modded Mag 2D, I'd go for the U2. It's smaller, has a better finish on it, and likely to be as bright as most single Luxeon Mag mods. The Mag has a bigger reflector and will almost certainly throw farther than the U2, especially if it has a Lux I/III in it.