I can't actually find it (which is ruddy irritating since I remember it so well), but basically what it came down to was that some of Nintendo's higher-ups (I think including Reggie?) weren't entirely happy with the direction E3 was taking, so they decided that, while they would continue to maintain a presence there for the mainstream press, they'd withdraw those titles aimed at the core fanbase and have them showcased in dedicated fan-oriented events until further notice.
I'm sure Nintendo is going to bust a gut this year trying to impress the mainstream press again, but with the old style of E3 back on the menu and the latter half of last year being pretty barren, I just can't see them holding out on us again.