We went to 26" due to tire availability in wider sizes in Argentina, on a Mocha Co-Pilot. Found an advantage of 26" when fitting the bike into the cases, gives you a little more space.
I have the impression that we could squeeze out a slightly higher top cruising speed on the 700c tandem, but have no scientific basis to prove it.
We went for a 54t x11t top gear, thinking that if we were infrequently using 54x12 on our old 700c tandem, we would need 54x11 on a 26". However in hindsight, I think we should have ordered it with 52x11, by the time we get to 54x11 we are going down a hill fast enough that we will be coasting. Some day I'll try the bike with two very strong riders to see what we can do.