RX rides better, handles better, brakes better, has much better style and an air suspension system. The quality of the materials on the inside are also much nicer.
MDX wins on space in the rear and third row seating if you need it. With the third row down, the MDX has at least 50% more space, so if you are hauling a lot of stuff, the MDX may be a better way to go. If you have less than two kids and care about the driving dynamics, you will be happier with the RX. I just purchased the RX after having driven a BMW X5 for the last three years and I love the RX.
You can get a similarly equipped MDX for about $3,000 less than the RX. The biggest difference to me, however, is that there are no side curtain airbags in the MDX, thus the RX is safer IMHO.
Good luck.