I love how some people here actually believe they know why Nintendo didn't show the Switch at E3. There could be a myriad of reasons.

Or maybe they wanted to focus mostly on Legend of Zelda during E3?

I'd say it was due to multiple reasons, one of the bigger ones being the console and games weren't ready yet. 2nd, they wouldn't want the NS overshadowing Zelda U. If they showed off the console and the list of games, along with Zelda, chances are it could lose some of that fire it got during E3, and Ninten wouldn't want that to happen. And 3, perhaps it just works better with the current plan they're going with. With how quick word travels, there's no need to reveal a console several months in advance. It can be done much closer to the launch date, and spreading the info out keeps the console in people's minds, so they're less likely to move on and forget it.

Because they were not yet sure what was going to happen. They weren't sure what they were actually going to reveal later in the year as it depended upon many different factors. In the end they decided to only go with a very limited reveal and show the rest in January, post holidays.

Because Nintendo works in mysterious ways.
...and because of Iwatas death and the impact it had on how business was handled.
...and because they did not want to kill 3DS that still sells both hardware and software (sun & moon).
...and because of shareholders that only wanted to hear about mobile games.
...and because they knew they had Pokémon GO, Mario Run and the Apple show coming up.
...and because they (once again) are focused on the Blue Ocean and do not care much for core gamers.

I'm guessing they had some changes needed since it would not impress the critics nor the fans..

No one will ever know.. D:

Because #1 they obviously didn't have anything ready to reveal about the console other than the most basic info about the hardware that the teaser reveal showed, and #2 why bother if the console isn't coming out until March 2017 anyway?

If the Switch was slated for this holiday, then Nintendo would have revealed it at E3 with 5 months to go till presumably a November launch. Instead they already announced it wasn't coming until March, and they decided to reveal it in October, which is 5 months from launch anyway, so it really makes no difference.

I honestly just think Nintendo is moving away from E3. I mean this isn't 1999 anymore we don't really need a load of journalists going to some convention then reading about it in some 5.99 magazine..... We just need youtube video and TV commercials. Also twitter, Facebook announcements etc

Perhaps they really wanted to focus on Zelda? It did work after all.

I think Nintendo is moving towards quicker, more viral marketing for their core audience, wich ironically for a company that usually gets accused of being behind the times, is a very modern approach.

As someone else said, focusing their whole marketing power on Zelda, the Switch launch title at E3 might have been risky, but it payed off big time. Everyone wants that game now, and you can get it on the Swich.
By not revealing it at E3 the also avoided some of the more direct comparisons to Sony and Mincrosoft.
I think Sony themselves might have had a similar strategy when it comes to the PS4 pro.

Also I think they might just not have been ready to show it off yet. The Switch is presumably powered by a custom version of the Tegra X2, wich at the time wasn't out yet.
Nine months until launch is actually a pretty long time for a console in developement, a lot of things are still subject to change at that point.
We only started hearing proper devkit rumors last october, 17 months from release. Before that any devs working wih the system likely only had virtual devkits. And the rumors only got more concrete in the second half of this year when presumably a second round of improved (maybe finalized) devkits was sent out.
We can tell they are diffrent iterations of the hardware by how the devs talked about them. 'Noisy, actively cooled' (likely Tegra X1 overclocked to get closer to teh custom X2 specs) to 'still a little noisy' (likely custom tegra X2 implemented).

And that is just hardware specification. Consumer product design especially for the asseccories as well as the controller might not have been finished until shortly before the trailer dropped. To be frank I don't think the pro controller they showed was quite finished even in the trailer.
The Joy-Cons, Joy-Con cradle, Dock and Swich itself looked pretty polished but the Pro-controller gave off a bit of a prototype vibe imo.

In short there are about a million reasons why they might have done it that way, and so far consumer goodwill and general excitement around the console proves them right. We will see if they can use that mometum in january.