Wrong. GameFreak alone are the development team behind the games, while Nintendo supplies the development kits and probably also contracted GameFreak to develop and Nintendo publish. The contract would be how you'll never see Pokémon on a non-Nintendo console, of course. But you're right at how Nintendo calls the shots as to publishing; they decide the pricing, too.
You all have to remember that Diamond/Pearl was a "first venture" out of the box for them. Not only would they spend development time with 3D, but they will have needed to develop a touch-screen interface for the first time. So, they'd have to find the best way to handle all that.
Pokémon roaming on the map could've been easily done, but wouldn't it be even more mysterious if you DIDN'T know what special Pokémon was lurking around? And the thing with Pokémon following around is that it requires someone to actually sit down and design every single Pokémon by hand. Not everyone has the time and money to bother with that… until now. If HeartGold/SoulSilver really was worked on for a few years, their headstart (since the games are REMAKES - the game's been laid out for them for a long time) means that they can spend more time implementing what they please. Get that?
More often than not, it's about development time more than anything. GameFreak works on more than just Pokémon, after all.