I think Nintendo was the only one who actually treated the new E3 like it is. They showed up to a barbecue wearing a t-shirt and jeans, while most others followed suit (Capcom showed up naked). Only a few companies showed up in tuxedos and wondered why everybody was staring at them.
I know it's hard to believe but E3 just isn't that important anymore. I know it has a long history as a business meeting and then a gamer's mecca and then back to a business meeting, but the times, they are a-changin'.
Its a strange sort of cognitive dissonance where you hold two ideas in your head:
1. E3 is the big gamer's meeting where all the guns will go off and companies should structure their developments and announcements around it.
2. Companies are starting to downplay E3's importance and don't feel compelled to bust out all their stops for it, treating it like it's "just another show"
When these ideas clash you will have a reaction, such as anger or sadness. Blame will be ascribed, and many felt Nintendo was to blame for E3's "lower-key" atmosphere, despite the obvious realities on the ground. And so, like good social businessmen, they apologized for not meeting expectations, even though they were expectations that they didn't engender. It happens all the time like when Japanese baseball players get injured and apologized for the fans for getting injured.