If you are going to be on the road that much there is no real reason to have 26" wheels on a tandem and several reasons not to.
1) Gearing-26" wheels with road tires are a lot smaller than 700C wheels. You will need much larger chainrings to get the top end gears you will likely need. If you are going to really do lots of steep climbs 26" wheels will allow for much lower gears but you will run out of top end gears sooner.
2) If you use rim brakes without a hub brake 26" wheels have a lot less surface area to absorb and dissapate the heat build-up. Blowing a tire is not a good thing-I know, we have done it.
3) Replacement parts and tires is not much of a consideration as it used to be so there is little to choose there.
4) Quality road tire selection. You will find a huge choice of durable and light road tires available in 700C. There are only a few really high performance road tires available in 26" (Panaracer and Continental) although there are lots of fairly wide wire bead hybrid tires that will do well for touring and more casual riding.
I bought a Cannondale tandem (MT-1000) a number of years ago at an end-of-season-super-sale through a LBS (I know the owner and the shop manager). It was a steal and we've enjoyed it. For general cruising, club rides and family fun it is a blast. Not fast, but rock solid on downhills. Slow on the flats when we try to keep pace with friends on their Santana.
Rolling resistance because of the fat slicks, weight of the rims (even though they are light MTB racing rims), and the mountain bike gearing will slow you down. It is easy to get "spun-out" on the flats or down a hill. I hope to change the chainrings someday, but it is a low priority now.
If I had to do it all over again I would get a 700c road bike tandem. The MTB tandem looks very cool. I've upgraded the brakes to Magura Hydraulic (tough to do on a road frame), and the bars are pretty comfy with bar ends for the captain and stoker positions. I'll keep the bike for now, but do wish for more speed at times.
I concur - go with the road tandem with 700c. You can always upgrade the tires for gravel and dirt roads.
My wife and I owned a Paramount tandem with 27" wheels and then bought a Rodriguez aluminum with 26" wheels. There was so much difference on the road that we sold the Rodriguez after 500 miles and bought a Santana Noventa (700c) and never even contemplated 26" wheels again for the road.
Gearing is a pain and finding lightweight rims and tires in 26" suitable for tandems is hard. We could only find heavy stuff for mtb or super light for time trialists.
Lastly, they seem to have higher rolling resistance and we always felt like we were pedaling through mud. If you're going to ride the road, get a road tandem.