Yes, indeed. I had exactly the same with my old system, which was quite similar to yours. Mine was an i7 920 overclocked to 4.1 GHz, together with 2x560ti SLI.
Now, the most straightforward answer would be CPU bottlenecking (although for reasons I will explain, I do not think this is the correct explanation). CPU bottlenecking would fit the facts: low GPU utilisation and low frame-rates suggests a CPU bottleneck. Plus, Skyrim's engine is known to be poorly optimised for quad core CPUs. You will normally see only 2 cores utilised, which in extremis will be around 90%+ on one core and only 30% on another. Cities stress the CPU because the geometry is quite complex, plus there are more NPCs meaning more AI calculations. Both of these are CPU tasks.
So, I had assumed my problem was a CPU bottleneck. But later investigation indicated that this was probably wrong.
My next build was based around a 2700k, which I overclocked to 4.8GHz. Initially, I kept my SLI 560 Tis and the experience was exactly the same: good frame rates out in the open, but lower frame rates in cities. If a CPU bottleneck had been the problem, I should have expected to see the problem somewhat relieved by having a faster CPU, but no. I saw no difference whatsoever.
The proof came when I replaced my 560Tis with a single 680. Most benchmarks will tell you that a single 680 has only slightly more power than 2 560 Tis so I wasn't expecting to see much difference. Indeed my only reason for upgrading to a 680 was with the intention of getting a second 680 later (which I have now done).
I was certainly not expecting to see what I saw. With a single 680, performance in Skyrim was on a different planet from my 560Tis. With all settings maxed (and with the hi res texture pack), frame rates in cities were now super smooth.
What could possibly be the explanation given that my 560s had been only 30 percent utilised while I was seeing choppy frame rates?
I cannot say for sure, but I think the explanation is the size of the VRAM. The 560 Tis only have 1GB while a 680 has 2GB. At max settings, this is not enough for a smooth experience in Skyrim. It would also explain why the GPU is not fully utilised. When the VRAM is the bottleneck, there is GPU power to spare.
So on the basis of my experience, I'd say flog your 560s and replace them with a single 680. You'll probably be glad you did.