People usually have this one sorted out before their conversation with us about wheels, but we get asked for our opinion on thru axle versus quick release all the time. Here are a few thoughts.
The two compelling things about thru axle are security of wheel to bike connection, and repeatability of rotor placement. With quick release disc builds, we've always supplied bolt on skewers rather than actual quick releases. This is because the brake force in a disc wheel pushes the wheel forward and down - out of the dropouts. On a rim brake wheel, that force goes in the opposite direction - up and back, into the dropouts. There's also the issue of the quick release lever potentially being next to a hot rotor. With a thru axle system, the entire axle goes - you guessed it - straight through the fork or frame, and the axle would have to come out before the wheel to bike connection was lost. It's harder to screw it up.
You might say "yeah, but only an idiot doesn't know how to use quick releases!" Guilty as charged, but my first time out with a new suspension fork several years ago nearly cost me my beautiful face, as the movement of the fork legs kept working the quick release loose. A bolt-on skewer stopped that issue cold, but from now on it's only thru axle suspension forks for me.
On a quick release hub, the knurls on the end cap faces bite into the frame or fork to make a secure connection with the hub. That works well, but the knurls never quite line themselves up perfectly each time you install the wheel. On your rim brake bikes, you might have noticed this once or twice, and fixed it by loosening and then re-closing the qr. With discs, the rotor's clearance between the pads is much less than a rim's clearance between rim brake pads, and that fit becomes more exacting. A thru axle set up is more precisely repeatable.
While my current road disc bike has quick release front and back, and they work just grand, if I was getting a new disc bike - road, cross, or mountain - it would definitely be a thru axle front. The decision on the rear gets a bit murkier.
The quick release standard for disc rears is to have the dropouts 135mm apart, with 10mm diameter dropouts. Already on road bikes, which often have chain stays about 405mm long, the 135mm spacing causes some friction. First, it's hard to keep your heels clear of hitting the wider-spread chainstays (especially when you're a duck-footed freak like me). Second, the chain line gets more tortured as you shift to the outer cogs. Shimano says you need a 420mm chainstay for their drive trains to work correctly on 135mm rears. Specialized goes so far as to move the drive side flanges inboard on many of their disc hubs so that you can use the full gear range even with a 405mm chainstay. The problems with that are that you're somewhat limited to their hubs with their bikes, and moving the inboard flange in is precisely what you don't want to do from the wheel's perspective. For what it's worth, you can totally use a normal hub in these Specialized bikes, you just don't want to do any small-to-small cross-chaining - even if you are Andy Schleck.
Thru axle rears generally have 142mm dropout spacing, with a 12mm axle rather than 10mm. With long chainstays, hey no problem. On road bikes, it simply ain't happening. The other thing is with the hub shell. Any hub that's convertible between 142x12 and 135x10 must use a hub shell that's limited to the flange spread allowed by 135mm dropouts. This is already pretty good, and you can build stellar wheels in 135mm-spaced flanges, but any benefit to the wheel structure from wide spread dropouts is almost always lost because the huge majority of hubs are convertible - as ours are.
So the rear is a little bit more complicated than the front, but I expect that I'll see a new 135mm thru axle "standard" for road bikes when I go to Interbike in September. We'll need to give White Industries a little time to make the kit, but our CLD would be able to handle that format. And I thought this blog would be shorter than it was. Sorry.