Yes, however ARM Cortex-A9 MPCore can support up to four cores. The current A5 SoC has two.
Thus, the Apple A6 could be a quad-core ARM Cortex-A9 MPCore based design.
AnandTech has a good article about what to expect from the A6 processor.
http://www.anandtech.com/show/4971/apple-iphone-4s-review-att-verizon/7 (note: numbers in this article are for the iPhone's A5 processor - the A5 processor in the iPad has higher clockspeeds).
It's really about expected that the A6 processor will be produced at a 28nm/32nm line (because Samsung and others are dumping the 45 nm line). This would allow a thinner, smaller processor which generates less heat and uses less energy. If Apple goes for a quad-core processor, it is very well possible it might use less energy than the current A5 processor.
If we look at the architecture, really anything is possible. Apple has never stuck on the same architecture for more than two generations, but it's too soon to get a good pattern. It will be either the Cortex A9 architecture or the Cortex A15 architecture.
CPU clock? No one really knows right now. If the A6 processor indeed turns out to be a quad-core processor, than it's likely it's clocked at 1 GHz for iPad 3 and 800 MHz for iPhone 6. If the A6 processor turns out to be, for example, a dual core cortex A15-processor, than it could stay clocked at 1 GHz (A15 architecture is faster than the A9 architecture at the same clock speed) or it could be higher.
There are really lots of possibilities for the A6 processor. Apple
could, however, play it very aggressively. Most companies try to avoid to move to a new process (like from 45 nm to 32 nm) ánd architecture at the same time. Apple, however, has already done so in the past: with the iPhone 3GS they moved from a 90nm process to 65nm process and they went from the ARM11 architecture to the Cortex A8 architecture.
If Apple is going to pull of a similar trick with the A6 processor, than that is great for us: the iPhone 3GS probably wouldn't have gotten iOS 5 if it had the old ARM11 architecture - even at the same clock speed. A new architecture would be very advantageous for us.
GPU wise? No one really knows.
I think that Apple really wanted to put a retina display in last year's iPad 2. If we're looking at the facts, the GPU in the iPad 2 is really powerful and it could have easily run a retina display while keeping the same performance.
The question is if Apple is going to do this again. Apple didn't change the GPU from iPhone 3GS to iPhone 4, yet the iPhone 4 pushes four times as many pixels. So iPad 3 might not become any more powerful, GPU wise, at all.
Obviously, I do hope Apple puts in a much better GPU: this allows for better performance at higher resolution.
