do you have tool box mounted in the bed? if so the answer is easy yakima.  with the tool box you have to mount the thule in a way that means that you can't lower it(due to wheel wells). 

If you don't have a tool box then the hard thinking comes into play.  I only raise up mine if I am carring a canoe or long boats.  I should say that I have a basket mounted to mine that gives me a six inch lift on one side.  mounting accessories can be a challenge but it is not a pain (usally requires a thule adaptor kit or a trip to the hardware store for longer bolts).
Both are nice the main advantages to the thule are that it raises up and down and has a higher weight capacity.  If you have the bars for yakima and the two previous features are not that important, save money and put it in the tank for a trip to the river.
I know that I didn't say anything that would sway you either way but they are both nice systems and both work very well.  if you add a basket be prepared to have lots of people ask 'what that thing is for?"
 both are easy to mount  as long as you don't have a drop in bed liner, that requires drilling the bed liner and not dropping anything :)

Todd