Didn't they pitch the idea to other publishers really early?
Well, even if my memory's faulty (probably is, ha ha), the thing is they didn't have to make it a GB game (which is what I'm driving at here). Then of course, once Pokémon came out, it was too late to jump ships.
I don't think Pokémon was pitched to anyone else, since the core idea was meant for Game Boy to begin with.
Game Freak has been involved with Nintendo through numerous other ways though. In the olden days, they worked on plenty Mario spin-offs, and they helped develop certain hardware (like Game Boy Camera). Some of their more recent (so to speak) non-Pokémon games are also Nintendo properties in the same way that Pokémon is. More importantly, many of their producers come from a Nintendo background.
They are also deeply affiliated with Ape/Creatures, a different independent company with a strong Nintendo history. Ape's founder Tsunekazu Ishihara is the president of TPC and majorly responsible for the franchise's success. Ironically, Satoshi Tajiri published a love/hate review for Mother (aka
Earthbound 0) when it first released, before establishing Game Freak as a game studio. He sounded equally critical and inspired by the game.
They are pretty independent though, and this project shows it. Sugimori never hid his love for Sega.