I wouldn't really care at all, expect for one thing. I use a 25' Monoprice HDMI between pre/pro and projector, and I really don't want to fish another 25' HDMI cable. For a 54" TV, assuming the components are all right there next to it, I honestly wouldn't care. I do not expect the 3D BDPs to
not have dual outputs for quite a while. Likewise, I still expect BDPs, 3D or not, to still have optical output for quite a while, for instance.
Also, one can have your separate calibration per source input?

3D via active shutter will need twice the brightness, right, or do I have that wrong . . . ?