I've got a full setup of each. The thule isn't as easy to get on and off, and I can never get it to line up perfectly. The yakima is better in that respect.
As far as value goes, I can't say because I bought both of my setups used. I think I've spent about $150 total and have 2 full racks, bike trays, locks, tons of spares, and a fairing. Craigslist is great for finding cheap roof racks.