Well, I think the luggage issue is a very valid point. Anyone who is on extended business in a region outside of his home airline (program) can suffer some big luggage charges.
I was thinking that as the alliance operating as a unit becomes more important in the market, that it makes sense the elite benefits be better aligned. I am of two minds on this, as for booking awards I am glad that only Flying Blue members are competing for P seats and getting extra Platinum availability, but on the other hand, it would be helpful to know that across airlines in the alliance I can count on really seeing concrete benefits in the travel experience from being E+.
At the same time, as there are more JV's and other sharing constructions established within Skyteam, it would seem that having greatly differing FF incentives could disrupt some of the JV profit sharing goals. The rather transparent and jerky attempts from Delta to turn Skymiles award redemption into a FB-style cash+miles system would seem to confirm that the programs are growing towards each other.