Don't know about Nintendo, but sources a few days ago were already reporting that MS had heard the rumors about Sony not attending, and were planning to step up their own conference accordingly. If those sources are true, I would expect a pretty big blowout from MS at E3, they'll probably announce a couple more 1st/2nd party games than they originally planned to, and they'll probably make it at least a half an hour longer than they originally planned to, since they'll need to make room for more 3rd parties now that the 3rd parties who don't do their own conferences have no other stage to announce their games on during E3 (unless Sony decides to do a State of Play stream during E3 or something).
Makes sense. I mean Microsoft and Sony are both launching new systems this year. And PS4 is actually not that far ahead of XB1 in North American sales. This is kind of Microsoft's opportunity to win back the NA market from Sony. There are definitely a lot of NA customers that could easily switch back to Microsoft.
As for Nintendo, I would double the length of their normal E3 presentation and show off more of their third party and indie games coming out. Normally their E3 presentation is 40-45 minutes. They could put another 40 or so minutes of third party games in that pretty easily. Switch gets more third party games each year than the last and it got over 1000 games last year.
Basically the time for Nintendo and Microsoft to fight the hardest is this year, because Sony is giving them an opportunity to screw up Sony's launch. They might as well take it.