There are many ways of defining "fair" - and in this case, one of them is to make it more likely that the person who cares enough to pay attention will get the upgrade over someone who doesn't care.
What happens with an automatic system when the latter gets the upgrade, but not the former? The obliviate still doesn't care, but you've now got someone in the back who's ticked off.
It seems to me that MSUs allow Delta to create a situation for its FFers that in some ways does give people a tiny sense of control - Seat1A mentioned declining an upgrade on a short flight - well, that frees up a seat for someone who might really want it anyway, and the person who voluntarily declines an upgrade is going to have a different attitude from the person who really wants it but can't get it. Yes, they could do a lot better (hint to Delta lurkers: letting folks convert unused MSUs to miles would make a lot of people happy and would cost DL veryvery little).
Even given that occasionally the attentive would-be upgrader is forced to miss the window, I think most people here would be far less happy with an automatic system, unlimited MSUs or not.
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