First of all, let us get this one little fact out of the way: Nobody "wins" E3's....there is no score board, no trophies, no achievements, nothing! So let us move on from this attempt to make this into a contest.
Second of all, both MS and Ninty's conferences were great for what they did. Microsoft announced games that we pretty much knew were coming for a long time (though MGS: Rising was pretty new and exciting), only now we have seen a couple of new videos with some gameplay (or the same if you have seen them online) and then they made their surprise announcement with Project Natal. Project Natal seems to be a prototype technology with not only minigames but also new aspects of controlling your console. The technology is new but is still unclear on exactly how traditional games can be played. Only the future can tell us this but Microsoft did an excellent job in creating hype and announcing this tech.
Nintendo had their own fantastic conference as well. Not only did they announce core games made by the third party, but they announced new games that we haven't even heard of...whereas MS announced Alan Wake, MW2, Splinter Cell, MGS: R, etc., Nintendo announced NSMB Wii, SMG2, GS DS, Metroid: Other M - games we haven't even heard of! - and much more! I think Nintendo did pretty damn good on their own...not to mention announcing and giving help to third party games in their announcements.
And to say Nintendo failed because of no Zelda Wii or Pikmin 3? That is just stupid, period. We already know it is coming...a video proving it exists isn't going to make it come any sooner. In fact, people will just ask why it isn't coming in now (like G4TV asked regarding SMG2). And second of all, lets watch the Sony conference to decide who won it all.