I agree but I think GameFreak should continue to make the top-down games as well. The top-down games are still be good enough for most fans and will be quicker to develop than a massive 3D game. These massive Pokemon games (let's call them Pokemon 3D) you're imagining will probably appear once per generation and have huge development costs. They also won't make as much profit if they end up selling as much as the top-down series. If Nintendo decides that the first Pokemon 3D game will only have Kanto Pokemon, and only Johto and Kanto Pokemon for the second (and so on for Gen III to infinity), than they have even more reason to continue their top-down games if only because those have more Pokemon. However, I think these Pokemon 3D games are better suited for home consoles to further protect each series sales.
In other words, treat Pokemon like Mario. The top-down Pokemon games will be like the New Super Mario Bros. games and the Pokemon 3D games will be like the 3D Mario games. If Nintendo has to expand or hire a new Pokemon developer team than do it! In the end, they will have another profitable series that fans will enjoy.
