1. Not enough variety in themes or game-play. I don't like platformers, for example, which make up a significant part of Nintendo's catalog.
2. Almost global emphasis on shallow characters and narratives. I understand they do this so they can keep their franchises "evergreen" but, as a consumer, I don't care about that. I like complexity.
3. Emphasis on gimmicky/innovative hardware and stable software. I like it the other way around.
4. Being behind the rest of the industry in terms of features like accounts and internet service yet trying to spin that as a good thing.
5. What's with the lack of internal memory?
6. Reggie is arrogant.
7. Fire Emblem should be on PC.
8. Third-party support. They fix that and it would go a long way toward helping some of the other issues, especially since I care more about third-party franchises than anyone's exclusives.
So, basically, Nintendo is a really poor fit for me personally. Even when I was a Nintendo fan, I wasn't into a lot of their games. Now that other consoles (and PC) fit my tastes better, Nintendo's home consoles haven't been that appealing.
Edit: After reading a few other posts--
9. Yeah, as a PC gamer, the thing with Nintendo prices never going down does not sit well with me. I almost never buy at full price.
10. Nintendo consoles pretty much being dead a year before they're replaced. That cuts a year off the functional life-span. Playstation has spoiled me in that regard.