I'd have to disagree. Zones has always been the most knockout heavy mode in the game, and thus games don't last as long as other modes. Having 2 zones helps to make a round last closer to the length of other modes by stretching out the neutral game. Dual zones is a good thing, the annoying part to you rather has to do with map design. A map like Umami ruins allows you to move on the map more freely and move forwards despite not having both zones. Flounder and Manta you hate because you have to move forward through the zones by capturing both of them (generally).
I think we need to see more of dual zones as it reduces the effectiveness of cheese strategies by requiring them to have coordination and balances out a more lock-out heavy mode. Just put it on better designed maps.