Relevent experience here (long)....
ganze,
I've got some experience with the setup you're trying to get. I had a disc brake equipped Gunnar built with the intention of running both 26" and 700c road wheels. I thought I'd designed the perfect all 'rounder style bike. Afterall, the circumference of a 26" wheel with a 2.1 tire is pretty much equal to that of a 700c wheel with a 23c tire. I decided I would build a couple sets of disc hubbed wheels, equip the bike with drop bars, then have the perfect do-anything bike. While it worked from a technical perspective, it wasn't a very good bike. Here's why...
For one, the high bottom bracket height, combined with the longer wheelbase, made for an ill-performing road bike. To take any turn at speed, I'd have to slow way down. The back end was unpredictable and when I'd hit any sand on the road, I'd begin to lose it. Of course sand is any road bike's enemy, but it was worse than usual on my Franken bike.
Off road, the bike was pretty good. I live in Indiana and it handled the flatish off roading pretty well. However, on any significantly steep climb, it was hard to get over the bars far enough.
As far as equipment goes, I set it up with Avid mtn. disc brakes and the Dia Compe Vbrake levers on drop bars. The drop bars I used were the Bontrager cyclocross bars that have a 25.4 clamp size. As far as I'm aware, they are the only 25.4 clamp drop bars presently available. They're real comfy and I use them on my cyclocross bike too. Ritchey makes some road bars with a 25.8 clamp that I'm pretty certain would work fine too. In fact, I have a set of 44's I'd be happy to sell you.
However, I had considerable difficulty getting my brakes to work properly with the Dia Compe levers. Once braking was applied, I couldn't get the Avid's to release and it seemed I was always riding with some drag on the brakes. I think the problem was a combination of 1) the use of Avid Flak Jacket brake cables. They were great for sealing gunk out of the cables, but they created lots of drag. 2) The return springs in the Avid disc brakes aren't as strong as regular Vbrakes and they don't want to return to the "open" position as readily as Vbrakes. 3) I also used cyclocross style top bar levers which probably also added drag. 4) Cable routing. On drop bars, the cables have more twists which further add to friction. Anyway, these things contributed to poor braking. I never experimented with changing any of these things but switched to Vbrakes and my problem was solved.
I've posted a picture of the bike in it's "road" trim. I think you can see that it looks a bit awkward with it's high BB. I would imagine that going with even larger wheels would have further exaggerated the high BB problem. If you'll notice, 29er frames have much lower BBs than 26" frames. BTW, I had a Cannondale Bad Boy and switched b/w 26" and 700c wheels with the same handling troubles.
I've ridden a Surly Karate Monkey with both road and off road wheels and it is, IMHO, a clearly superior bike. It won't ride like a road bike, but it's close enough that I'm happy with it. It rides off road better than my cyclocross bike. If you're looking for only one, do-it-all bike, a 29er with two sets of wheels is MUCH better than a 26er with both sizes.
Good luck and have fun.