The R540 is what I'm using now. I just started hearing what I thought to be bearing wear, and was looking to get the Ultegra since Shimano's literature seemed to imply that the Ultegra had different (and replaceable) bearings. But looking at the R540 literature, it looks like the bearings are the same as they are on the 105 and Ultegra models:

http://bike.shimano.com/media/techdo...9830608623.pdf

What does appear to be different is that the R540 has a plastic skid plate (the body cover (4) in the drawing) that is not only replaceable, it wears out and must be replaced. The 105 and Ultegra appear to use a steel plate that shouldn't need replacement.

I'm starting to think that the clicking noise is either the body cover or worn cleats.

BTW, although they are not the lightest thing in the world, I do like the SPD-SL system. They're very secure when riding, give a wide platform, and you can actually walk in them without risking an impromptu Irish jig on hard floors.