Sure was worth it, and they sure were "ready to show" https://pbs.twimg.com/media/CvVuGDmUkAMaxOL.jpg:large

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.

I still personally prefered the Skyward Sword Wii U reveal E3. That was stuff of Legends!