Total conjecture on my part, but you've got all the executives from Nintendo, Game Freak, and TPC itself (maybe Creatures too?) all with their own priorities and who might not necessarily want the same thing at the same time.
I can see how that might create some pressure to just kick a product out the door rather than negotiate with all the different stakeholders about whether to delay, how long to delay, etc. etc.
it could also be as simple as Pokémon being the most Mass Media Property under the Nintendo umbrella. I think about that in comparison to Zelda, which has always sold well for Nintendo but has never been the commercial juggernaut that Pokémon is.
What Zelda has had for a long time is a relative prestige attached to it compared to Pokémon, which might help with allowing teams a protracted development period. Part of the purpose of Zelda is to be a critical darling and a crown jewel in the library of the console.