You could give 'custom lights' or hyrbrid strings a try.
For instance, I always use Dean Markley Custom Lights...

9, 11, 16, 26, 36, 46

It gives you a light gauge on the top strings and a slightly heavier gauge on the bottom ones. (also good for guys like me who tend to play really heavy rock but need lighter strings for tapping and leads)

You could also try just raising your bridge on the bottom strings slightly.
However, don't forget to redo your intonation afterwards.