Coming from a Polygon interview with Reggie Fils-Aime...
"It was not an apology. It was not a statement about the content we're showing, essentially it was an 'I hear you' message. Mr. Iwata is in Japan and what he's trying to do is help explain to consumers in Japan what's going on at E3. The correct translation of his message was: 'Thank you for your feedback. We hear you and we are committed to continuing to meet your expectations,' was essentially his message.
(Concerning the reaction to Metroid Prime: Federation Force) One of the things I find interesting is that if you look at E3 historically for Nintendo, typically what happens is a press briefing happens or our digital event happens and then over the course of the next couple of days people see the games get to play the games and the appreciation and understanding of what we're doing increases over those three days and continues to build into the holidays.
Splatoon is a game that people are loving right now, but if you rewind to E3 last year, Splatoon was being viewed as, 'Yes, it's innovative and it's different, but the controls are a little hard and I don't understand the mechanic of turning into a squid and going through the ink.' There were all of these complaints. But now you look at the finished product and the satisfaction is huge. For us, our goal is to make sure we announce the content, help people understand the content, but most importantly get hands on with the games. I haven't heard the feedback (for this year's Best Buy demonstrations), but I think the feedback is going to be quite positive because what we do is make great games and they show well and they really lead to consumer excitement."