Now, this is all my opinion, so don't get up in arms against me, but there's so many threads about what's great (and it was great), but there are some things that I wasn't too thrilled with..
First off, the GameCube and GBA *barely* got any mention. In fact, I don't think the GBA was mentioned at all.
Second - two versions of Zelda? At least, we can probably assume the Deluxe edition will contain both. And finally our chance to get a game that people in Japan want.

But seriously, ouch. this hurts my wallet.
Speaking of Wallet - Third. I want a Wii... but I'm not sold on it yet. I need the price. Now I wasn't really expecting to see the price today, but I wanted it. I need to know how much to save up. Guess I can just save up $600 and if all else fails, buy a PS3. heh.
Fourth. Smash Bros. Yeah, I went there.
Fifth - hardly any mention of the online aspects. Sure, it's "on all the time". Yay. Couldn't care much either way (until something really neat is shown with that) Networking code in the console? IN theory, this would make online game programming as easy as programming a second player on the NES, right? Expand on that a little more, if you would. Most importnatly, barely a mention on the Virtual Console. Details pls.
Sixth. Nintendo, you told me that I'd understand the Wii name after the E3 conference. I'm still waiting.
Finally... ummm... wasn't there a "big" hardware secret supposed to be revealed today? Speaker? neat. not big. Always on? You've still got to convince me of that.
Did you decide not to show it for fear of Sony stealing it? That's fine, I'm a reasonable man... just tell me that.
Oh Nintendo, you do tease. I want a Wii, so badly, and you taunt me with such glory, but rarely put out.
Aside from that, Mario vs. DK 2. Kick ass.