Either will work, I wouldn't bother doing different patterns per side/end as the benefit is negligible. I'd definitely go 3X if the hubs are small flange, and I'd probably lean 2X with large flange hubs, especially if you're using deep rims.
Shimano hubs, shallow rims, and I hadn't really considered the extra torsional load that disc brakes would input when mixing up the lacing patterns, so 3 cross all round would make more sense.
2 or 3 cross on a 28 spoke wheelset?
I'm thinking 3 cross on the drive side rear, and 2 everywhere else would be best. Make sense?