I agree simply an overclocked 32nm A5 doesn't seem to work. The die sizes work out to be:
122.6 mm2 for the 45nm A5
69.6 mm2 for the 32nm A5
165 mm2 for the 45nm A5X
93.7 mm2 for a 32nm A5X (assuming the same scaling factor that the A5 achieved)
95.6 mm2 if the A6 is 78% the size of the A5.
There would seem to be too much extra area for the A6 to simply be largely a 32nm A5 with doubled clock speeds for the CPU and GPU. The 32nm A5 is only 73% the size of the A6. Apple confirmed a new ISP and a new memory controller to support LPDDR3 is probably a safe bet, but would those really add that much extra space compared to the 32nm A5?
The A6 is very close in size to a 32nm A5X and it's quite possible Apple swapped the 4x32-bit LPDDR2 memory controller for a 2x32-bit LPDDR3 memory controller which should give some space savings for the improved ISP and other tweaks. Previous Apple SoC have usually been thought to use a 4x clock speed differential between the CPU and GPU so this would be the first time they move to a 8x divider assuming the CPU is clocked at 1.6GHz while the SGX543MP4 needs to remain at 200MHz to match Apple's claim that GPU performance only increased 2x.
My personal theory preference would be that A5/A5X to A6 does mean something more generational than just clock speed differences and since the 4x CPU/GPU clock speed difference has always been in place, my default thought is that it'll remain so although I have no justification or advantage for that other than momentum and that it limits the possibilities of what the A6 can be so I can settle on an estimate. I also don't think Apple is roping in flash I/O improvements when they claim a "2x faster CPU" rather that really does refer to CPU itself. Assuming those limitations, my guess is that the A6 is a 1.2GHz Cortex A15 with either a 300MHz SGX543MP3 or a 300MHz SGX554MP2 and a 2x32-bit LPDDR3 memory controller. That could satisfy the 2x CPU speed, 2x graphics speed, die size differences, A6 meaning a generational change, and a 4x CPU/GPU clock speed difference.