It seems like you'd run into a lot of miscellaneous problems with this sort of system. When you make your water changes, you most likely have to siphon the water again to make the "water bridge" since the tubes to not go very far below the water level. Algae is also another issue that people may face.
The fish Highway is an amazing idea and the pictures are incredible. I bet it's such a pain to keep clean though. Would the tanks have their own separate filttarion systems or would there be a current developed where one tank is the drain tank and teh other is the return tank.
Also, bubbles will likely get into the Fish Highway and would be the biigest pain in the but to get rid of. Heh, imagine if something DIED in the highway and there was no current to get it out...