"Metroid Prime" at the E3 2014 fuels a lot of speculative fire. As of the moment, everything Nintendo announced loosely suggests that Retro Studios is already working on a new Metroid game for the Wii U. If this is true, there is a fair chance that Nintendo will announce the game at E3.
The wait for the "Metroid Prime 4" has been quite a while. In fact, the "Metroid Prime 3: Corruption" was released a several years ago already, way back in 2007. All three games were developed by Nintendo's first-party American studio, Retro Studios and were equally excellent. On the other hand, "Metroid: Other M," which was released in 2010 by Team Ninja did not perform as well, both creatively and financially.
Since then, Retro Studios made "Donkey Kong Country Returns" for Wii, a number of courses and modes in "Mario Kart 7" and "Donkey Kong Country: Tropical Freeze" for Wii U. The latter game came out this Feb., by which Retro Studios already started on its new project.
Thus far, that new project has already been in progress for at least six months is likely to be some sort of Metroid game as Miyamoto also hinted so.
However, Retro Studio's new Metroid project is not necessarily "Metroid Prime 4." As a matter of fact, "Metroid Prime HD" is more possible. In the past, Nintendo made remarks in creating HD remakes for Wii U similar to the "Wind Waker H." HD remakes were embraced by fans positively and did a pretty good job.
Interestingly, Retro has previous experience from "DKC: TF," but that is apparently a different beast from the Metroid. However, a HD remake will still give them the chance to test the waters for the system capabilities in the context of Metroid.
If Retro Studios is really working on "Metroid Prime 4," it is unlikely to hear news about it at E3 2014. On the other hand, if it is working on a "Metroid Prime HD" remake it is sure to make noise at the E3 2014 and it's likely to hit the shelves early next year.