To be fair, E3 is dying down as less and less companies care for it. So Zelda being the main focus makes sense. For Example, Activison and another company( can't think of who atm), are not doing an E3 show either. Also day 1 of E3 has a Nintendo Direct listed, so we shall see what comes of that. There is also several unannounced leaked games for Nintendo such as N Stars, so we will see what happens there.
And honestly you shouldn't fret over E3. It's losing it's appeal. No company needs E3 in this day and age. It's why they limited passes for non press, why you see less of a focus on it, and more. Also outside of the core internet, no one really knows of E3. I've known many gamers who had no idea what that was( and they were big gamers) until I told them. And most on the internet don't really know of it either. a lot of people will just check their preferred news site for news everyday, rather then watch live.
Another thing to consider, the gaming community has a massive casual fanbase. The core fans always underestimate the size of the casuals. Just look at Smash bros. Bayonneta is a big casual character that people who just played games loved, hence why she won the ballot. The core fanbase didn't think of it though, and were angry at first.
But my point there, is that companies like Nintendo are starting to realize that they don't need to waste time and money on E3 to sell their products.
Let's look at our first Sun and Moon info. We get a big trailer the size of XY's XY had an entire direct to build up that trailer. This time, all Masuda did,, was announce that news was coming on twitter, and setup a countdown for every language to used, and just reminded people every few days. The announcement spread like wild fire across twitter and other medias. The reveal was streamed by poketubers and had as many, if not more people aware of it then XY's Direct. The hype even seemed to reach to higher levels. This form of announcing stuff is probably why Masuda's doing it again. Nintendo is probably realizing that this is a pretty good way of doing things and I wouldn't be surprised to see it used again.
It's why Zelda is the main event at E3. It's a big title that always makes lots of money and has been wanted by fans for a long time. So now they are giving out details at E3, so they have a draw, but they don't to make their show anything else, as they have many ways to reveal info. I also wouldn't put it past them to focus more on the Tokyo Game show instead of E3 in future.
So to sum it up, don't be upset by their E3 lineup, it's just not a venue that screams big anymore, so companies are becoming less and less interested in it, and finding other ways to announce news.