I haven't actually used my rack yet (only had the 4Runner for 11 days) but the rails look very sturdy to me. The factory crossbars are usually the weak point.
I use the Yakima system already. I bought the RailGrab feet and 48" bars years ago to hold my RockyMounts. I've had them on three vehicles now. Very easy to adjust between different vehicles, and I can put the rack on my Volkswagen in 5-10 minutes, and it has the same type of rails. I would recommend it based on my experience so far.
For bikes, I will probably be using a hitch rack with the 4R because I'm not crazy about putting my 29er on the roof, let alone 4 of them. I dropped a handlebar on my Legacy and put a nice dent in the roof just before I traded it for my Volkswagen. I don't want to risk that on the 4Runner.
However, I will be picking up another set of (longer) bars at some point because I'd like to get back into kayaking. Time to cash in my REI dividend during the 20% off member sale.