A day without a Nexus rumor is like a day without sunshine
There's been a rash of rumors the past few days about an unannounced 5.9-inch phone from Motorola (see Android Police and The Information for their excellent coverage of all of this), and most of them say that this device will be the Nexus 6. What you've probably heard is that the Motorola Shamu, based on an entry in Google's bug-tracker system, is the next Nexus, and ready to take on the also unannounced iPhone 6, and we will see it shortly after the Apple announcement.
Like most rumors, this is surely based on some sort of proof, but a lot of it just doesn't make sense and we're not yet ready to declare anything as the next Nexus.
We know that the Nexus program isn't dead. Last month head of Android engineering Dave Burke spelled it all out with a single quote: "There is no way you can build the open source code without the phone or tablet or whatever you are building." Notice he said phone or tablet, and we're pretty sure that a new Nexus tablet is — and has been — in development. A new Nexus device will be the reference for the next version of Android, and having one is a necessity. Burke knows his stuff.
The issue comes when you consider that the next Nexus device(s) will be designed as references for the new platform. The reference device for Android L needs one very important thing — support at the processor level for 64-bit Android. We know NVIDIA is there, with the ARM-based Tegra K1. We're also pretty sure that this processor wasn't designed for phones, and chances are this is what we'll see in the new Nexus tablet.
Another reference device certainly is likely. The question is what. And when.
Qualcomm has the 808 and 810 just about ready, but those aren't scheduled to be released to manufacturers until 2015. In a completely separate but just as convoluted rumor mill, people are saying those will be held back for devices in the far east where processor specs are more important as a selling point. This means that any Nexus device using this CPU won't be available this fall when the iPhone 6 is announced, and the next Nexus devices are expected.
That leaves us with Intel. Intel has been making 64-bit processors since forever, and they already have a proven track-record in Android devices with their ARM alternatives. In fact, Lenovo and Motorola have built Android devices with Intel processors. This could be a possibility, but I have a gut feeling that Google would rather have an ARM processor as their reference CPU than an Intel x86-64 inside. This also says nothing about any other things handled by the modern smartphone CPU, like telephone modems or Wifi or GPS. Having these "on-board" is why your current smartphone has better battery life than the first LTE phones, which required a separate modem. Remember the HTC Thunderbolt? Yeah. The new 64-bit mobile chips from Intel do look pretty awesome, but we think they will need to be tested and refined in tablets before they get put in a phone.
So back to the Shamu rumors. If this is to be the next Nexus phone, and if it's to be released this fall to "compete" with a new iPhone, it will mean that Google got early access to Qualcomm's new products, or it will sport a new and unproven Intel chip, or that it won't be a very good reference device because it's not 64-bit. Anything is possible, but sometimes the rumors just don't all add up.

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