If were to run 4e, I would base off of Fort, Ref,and Will. If a player want to ignore certain stats, they should pay the price- my opinion of course.
If you base those three off one specific stat in each pair, rather than the higher stat in each pair, you're basically rewarding certain classes. You punish people for ignoring Wisdom if they have a Charisma-heavy class like the bard, but you're not doling out an equivalent punishment for people who ignore Charisma and take a Wisdom-heavy class like the cleric.
Which is your prerogative, of course, but I think it's actually a good move on their part to make all stats equally useful. Having a high Charisma and low Wisdom might be a great roleplaying move, and I think it's balanced out quite nicely by, say, the low-Wisdom character's lower Insight, Perception and other skills. The need to penalize the character in combat just seems unnecessary.