There are pros & cons to each.
With 5/4x6, you could get away with less joists/joist hangers, and, consequently, less screws/labor.
5/4x6 is heavier, and harder to cut, predrill, and bowrench into place...so there is more labor involved.
I stopped using 5/4x6 years ago. Cost was a big factor.
You have to decide for yourself.

steve

have you found more cupping with the 1x6 (as was predicted by the lumber yard rep), or is that taken care of with the additional joists, etc?

Cupping isn't an issue if you screw the wood down correctly, and have proper ventilation.

steve