Once the road construction and park issues are sorted out I think that Flood Park will be much nicer! Regardless, the Willows neighborhood tends to be more charming overall.. and it tends to be a little further away from 101. Not a dramatic difference.
Hope this helps!
The Willows tend to be more expensive than Flood Park for several reasons. It is closer to downtown Palo Alto and downtown Menlo Park. It is a larger neighborhood so there are more streets that do not hear any or much noise than Flood Park. Flood park tends to be noisier than most but not all of the Willows so that affects value. While nether neighborhood has a lot of new or newer construction there is more in the Willows.