The V1200 is deeper than the V1000 -- that's the only major difference.
The extra depth manifests in the motherboard area (more space between the drive rack and motherboard) and in the power supply area. You can fit a wider range of power supplies in the V1200 than in the V1000, and you will have an easier time routing the power cables for a normal sized power supply in the V1200. The V1200 also has an extra cutout in the "floor" of the motherboard "chamber" that you can route cables through.
I guess the other difference is that pre-cut window panels are harder to find for the V1200 than for the V1000, if that kind of thing matters to you.
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