Before the New 2nd generation Nexus 7 was released there was much chitchat about whether the processor inside was going to be a Snapdragon S4 Pro or the newer Snapdragon S600. Officially, on release we were told that indeed the older, Snapdragon S4 Pro was the processor being used, despite benchmark scores repeatedly showing the speed of the new Nexus 7 to be positioned faster than any S4 Pro before and in fact right in the middle of the pack of Snapdragon 600 scores. In fact, on paper many have noted that the new Nexus 7 has almost identical internals as the Nexus 4 phone and thus there's been some confusion as to why the new Nexus 7 repeatedly scores above its sister handset. Well there's a reason for that if you follow the logic of the tech gurus at both highly regarded tech blogs AnandTech and Arstechnica: The processor in the New Nexus 7 is really an underclocked Snapdragon S600.
While I have links below to the long version of the explanation, here's the pertinent material quoted to explain why this is so...
From ArsTechnica:
In our previous article, we noted that the 2013 Nexus 7 was consistently faster than the Nexus 4 despite the fact that the two ostensibly share the same system-on-a-chip (SoC). We posited that the differences came down to three things: additional optimizations in Android 4.3, differing thermal constraints, and faster RAM. All three of these are true—the Nexus 4 gets a measurable performance boost from Android 4.3, the new Nexus 7 doesn't appear to have the speed throttling problems that the phone continues to have, and the Nexus 4 uses slightly slower LPDDR2 rather than DDR3L. There's one more issue: these two Snapdragon S4 Pros are not in fact the same chip.
Sleuthing by AnandTech's Brian Klug found that the 2013 Nexus 7's SoC had a part number of APQ8064-1AA, compared to APQ8064 for the Nexus 4's SoC. That extra 1AA denotes a chip that is essentially a lower-clocked Snapdragon 600, complete with the newer and slightly more efficient Krait 300 CPU architecture. The Snapdragon 600 SoCs we've seen so far have been 1.7GHz and 1.9GHz variants, but because of the lower 1.5GHz clock speed, Qualcomm has apparently decided to fudge its branding a bit and slap the older S4 moniker on what is actually a newer chip.
From AnandTech:
the new Nexus 7 switches to Qualcomm’s APQ8064–1AA, a version with 4 Krait 300 CPU cores (yes, Krait 300, not 200) running at up to 1.5 GHz and Adreno 320 graphics. Rather than use a PoP and LPDDR2, this specific APQ8064 variant goes to PCDDR3L–1600 MHz instead, including 4, 4Gb discrete 1.35V SK-hynix DRAM devices off to the side (more on the opposite side of the PCB) adding up to 2 GB of RAM. Qualcomm's Snapdragon S4 Pro and Snapdragon 600 branding gets confused here, although Qualcomm is calling the APQ8064 inside the Nexus 7 (2013) S4 Pro, it's more like an underclocked or lower binned Snapdragon 600.
So basically what we have here is a Snapdragon 600 in sheep's clothing. Perhaps the clockspeed of the chip was lowered in order to conserve battery life and Asus insisted on using the Snapdragon S4 Pro branding in order to distinguish its S600 to other vendors. Perhaps there's some other reason but for all intents and purposes it does seem that the processor in the new Nexus 7 is punching above the typical S4 Pro weightclass. Thus perhaps we should just call it a unique one-off processor that was optimized for the New Nexus 7. You can read tons more about the tech nitty gritty as well as all the benchmarks you can throw a stick at by reading both ArsTechnica's and AnandTech's reviews (both glowing by the way) of the New Nexus 7 at the links below.