[Kovner]

How about - instead of increasing your check behind when made frequency, you increase your bet when not made frequency. Most of the time in 6max (or less), when you have position HU and get checked to, you raised preflop. If you only check behind in this spot if you're essentially giving up on the hand, than you do not need to worry about them beind exploitable (by giving on the hand, you are giving permission to exploit, and that is fine). You'll get more action on your made hands this way and you'll win a lot of 2 bet pots this way.
This is basically the reason why we are told to play aggressively in shorthanded limit.

If someone starts checkraising you way too often, you have to take free turn cards with drawing hands and invite the checkraises with made hands.