I disagree that a genome must be fully annotated for it to be useful but I do understand the point you are making.

I guess I am just more of an optimist when it comes to possibilities. If someone had the means and motive to put a WT on something like a 454 FLX or an Illumina HiSeq that would provide a reference. Then, using some of the cheaper TGS available and 4GS that are coming down the pipe (especially if OxfordNanopore lives up to the hype), one could rapid fire the morphs. Run alignments and you should be able to find the locus. You do not need to know the gene, the operon, the function or any of that, just find the difference.

Like you, I do not imagine it will happen any time soon, after all how many PIs are out there studying the genetics of ball pythons? But I do not think it is some epic project that defies the mind of mere mortals.

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