Would it matter if my miner was hashing random vs incremental values?
For a good hash function, like Skein, diversity of inputs has no impact on diversity of outputs. So, if you have no information about the space of possible pre-images (e.g., it is not a human generated password, it is a completely random input from your prospective), then the expected number of attempts before retrieving the pre-image is the same in either case. Should also be the same number of attempts to find an input with a specific hamming-weight from the input.

As you note, however, there are benefits to using the counter. You can easily save state. You know you will never see the same input. If you are generating random 64-bit values, the odds of seeing a colliding input is actually not as small as you would think. You would expect to see a collision after $2^{32}$ inputs.