I think the continent system looks great! It really complements on the exploration theme of the mystery dungeon games. I'm excited to have such a nice big world to explore.
From the sounds of it, there's going to be different shops and a different set of dungeons in each continent. I'm thinking there will probably be other differences too, like style and design, like Ben said.
I'm going to say that the Cloud Continent looks the best to me. I love the way it looks from its artwork, and from what I read, it's based on the explorable area of Gates to Infinity, which is a plus for me!
Since each continent is based on a different element, I'd expect the Pokemon found there to match the continent's element. E.g. rock and ground types in the sand continent, grass types in the forest continent, etc. But since the game is going to include all 720 Pokemon in the national dex, there's probably going to be a lot of variety in each continent as well.
♥Paired with Dragon and Koakuma