Have you looked into Malibu's new headunit? It's a Rockford and it fits into the same opening as your JBL. I went to AWS's Malibu demo on Saturday and rode in a 2010 Wakesetter LSV (just for fun... don't get any ideas). It had the new Rockerford head unit in it. Radich told me they switched to this unit half way through the 2010 builds. The reason I mention it is because while out on the water, we discovered something pretty cool about it... it has automatic speed sensative volume control. As the boat speeds up or slows down, you can see and hear the head unit adjusting the volume to compensate for the noise from wind, engine, etc.
It's kind of cool to have your stereo volume go down automatically after your rider goes down and you turn around to go get them. You should check it out.
Is your main concern the iPod integration? What's the issue with the JBL? Does it only play the older units or something?