I think one program will definitely simplify things, but I can see some things coming down the pike that will cause heartburn for many of us.
a) how will upgrades (electronic, miles, certificates) be rationalized across the carriers when some give them (quite freely) and some are adamantly against them (BA/QF).
b) elite qualification - is markedly different depending on the carrier. I think rationalization will result in even higher qualification levels, undoubtedly based on mileage and fare paid.
c) bonuses - likely to diminish or disappear completely.
Food for thought...