Good advice so far, especially not to skip holes on the rim. But that's not what you were asking. Skipping holes on the hub isn't a structural problem. It's a length problem, as previously noted, and solving for the odd lengths will either be a rather complicated mathematical problem or a trial-and-error one. If you're up for it, and you have a spoke threader, go for it.
There are non-standard patterns that allow mismatched hub and rim drillings. Most are crow's-foot style or crossed drive/radial non-drive.

Even building a Xh rim to a 2Xh hub (for example, 16 to 32) creates that problem. The offsets between hub flange holes mean you will need two different lengths for each side of the hub. And it won't be perfectly symmetric.