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Is the AT so much better hand than A3 that it makes the push better, or is it the dead money already in the pot with AT?

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Both. AT is about my cutoff point for pwning limpers. Ocassionally someone will have limped a monster or a better ace. But weaker aces call frequently, as will smaller pairs. Both of those villain hands will be favored against A3, but dogs or races against AT. The dead money more than makes up for the times you're against an underpair.

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.. or do I actually have less FE in A3 hand?

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Against a loose player, your FE in hand #1 is very small, because villain will still have a decent stack even if he loses. That's his thought process, though not necessarily the right one.