First off, Zelda II is not a bad game. I wouldn't say its better than the original like some people in this thread, as I still think the original is one of the best Zelda games out there and one of the most important games ever made. However, its still a good game. It has its flaws. Namely the lack of information of where to go and bosses walking off screen. And a impossibly hard last area which takes lots of memorization and skill to beat. But its still one of the better NES games.
As for what is an actual 'bad' Nintendo game, I can't think of many.
Maybe Gumshoe on the NES. An old game where you have to keep a perpetually walking character alive by shooting him with the NES Zapper. It pains me to say that however since Metroid creator Yoshio Sakamoto made that game. But it does have many flaws.
Another could possibly be Pokemon Colosseum. And retroactively Pokemon XD and Pokemon Battle Revolution. All of which had bugs, lacked features even the GBA/DS versions of Pokemon had and were far too slow to play. But most importantly, lacked any motivation to making you want to play a Console Pokemon game, which even Pokemon Stadium on the N64 did. Even Pokemon Battle Revolution was a worse game than Pokemon Stadium, and that's on the Wii! Genius Sonority, the developer of all three of those games, should really get its act together...or Nintendo should consider disbanding them.
Most of the other games I can think of that weren't that great I just consider due to personal reasons.