This is what they said:
At E3 we had very specific announcements that we wanted to focus on. We had a lot of things to talk about, and we had to decide which things were most appropriate for each method of announcement. E3 is just one of the many opportunities for companies to make announcements, and we’re always looking for the most appropriate ways to both inform and surprise consumers.
But that’s just how they’re spinning it. The real answer, I think, is that Nintendo wants more control over how and when they announce whatever they want to announce. The reliance on E3 forces them to announce things at the same time every year. That doesn’t always make the most sense though. As such, they’re “training” us to expect big announcements via the Nintendo Direct broadcasts. That means they can announce things when it suits them, rather than on any sort of external schedule. Or at least, that’s how I see it.