You're going some distance out of your way to visit East Palo Alto, where the roads aren't in great condition. Personally, I would cut through Menlo Park and cross 101 at Willow Rd (or the pedestrian bridge near Willow Road). Then take the Bryant bicycle boulevard through Palo Alto, Middlefield Rd (or California St) through Mountain View, and pick up your route in Sunnyvale.
The street in East P.A. that seems really bad is University Ave itself -- I cut off of it as early as possible, the right southbound curb there is horrible to be sure!
You mean a route like this? http://www.endomondo.com/workouts/oXGt10qCARU - because oddly enough it recorded as slightly longer (though I did stop at Palo Alto Bikes that day). Is there a better way through Menlo Park, perhaps? (I've tried a way that cuts through closer to El Camino and behind the Target store a couple of times...)