The Vortex Stone does not show up in the team toolbox.
Legendary Island is split into three smaller islands representing Articuno, Zapdos, and Moltres. All three islands are connected by a bridge. Moltres's island is represented with a volcano, Articuno's with a mountain covered with snow, and Zapdos's with a simple field. Each island has what appears to be a small temple on it, which are very similar to those used to store the spheres in The Power of One.