Is there a cost? Of course. But arguably it's in the noise on these chips. Knights Ferry and Corner are using a scalar x86 core derived from the P54C. How many transistors was that? About 3.3 million. By contrast, Nvidia's 16-core Fermi is a 3 billion transistor design. (No, Fermi doesn't have 512 cores, that's a marketing number based on declaring that a SIMD lane is a "cuda core", if we do the same trick with MIC we start doing 50+ cores * 16 wide and claiming 800 cores).
How can we resolve this dissonance? Easy -- ignoring the fixed function and graphics only parts of Fermi, most of the transistors are going to be in the caches, the floating point units and the interconnect. These are places MIC will also spend billions of transistors but they're not carrying legacy dead weight from x86 history -- the FPU is 16 wide by definition must have a new ISA. The cost of the scalar cores will not be remotely dominant.
I'm not sure why you are concerned about the pin count on the processor, except perhaps if you are complaining about changing socket designs which is a different argument. The i7 2600 would fit in a LGA 1155 (i.e. 1155 pins) whereas Fermi was using a 1981 pin design on the compute SKUs. The sandy bridge CPU design is a fine one. The GPU is rapidly improving (e.g. ivy bridge should be significantly better, and will be a 1.4 billion transistor design in the same 22nm as Knights Corner).