I also think that was a sort of period where nobody was really getting what they wanted from Nintendo. Japan didn't like Metroid Prime, Fusion's linearity wasn't taken well. Pokémon generations 3 and 4 are almost unanimously regarded as the series' lower points, many players declaring they stopped after or before Ruby and Sapphire. It took a long time for The Wind Waker to get its due respect. And, of course, this was Mario's rut of spin-offs. Sunshine was the closest we had to a new Super Mario Bros until... well, New Super Mario Bros. for the ten years following Mario 64. A REMAKE of SM64 came out before a second proper sequel did. Holy crap. Granted, the early aughts brought us what in my humble opinion were and remain the three best Mario RPGs all in a row (PM1, M&L:SS, PM2) and I do love both Luigi's Mansions, but I haven't been disappointed with a Super Mario [rest of title here] or felt like grumbling "
Another Party and
another Golf game?" in a good long time. That is how I like it.
Nintendo's weakness may still simply be their lack of third-party support. They're right about one thing, they have loyal fans who will buy a Nintendo console because, naturally, it has a lot of exclusives. But adult gamers who want to play a little bit of everything also need to take their pick from 360, PS3 or PC just to play all those games that are on every system except Wii/Wii U. I know I wouldn't bother if I didn't have to... but I don't really mind it this way, either, and competition is good.
I'll not hesitate to take the Wii U version of
any game I'm ever interested in (barring simply awful ports), though, because I just love making Miiverse screenshot & drawing posts that much.