Many homeowners living near the Caltrain tracks have been wanting the High Speed Rail to be built in a way which improves their neighborhoods. Trenched, tunneled, and raised tracks have all been discussed. A recent blog post probably shows the future. It looks like raised tracks are likely in south Palo Alto.
The Caltrain HSR Compatibility Blog posted an article on Dec 29, 2012 titled “Grade Separation: The Decadal View” showing expected changes to railroad crossings. The blog can be reached at: http://caltrain-hsr.blogspot.com/
The first phase is simply to complete the San Mateo/San Bruno grade separation in 2013.
The second phase shows four at grade crossings in San Mateo County being changed to grade separation by a combination of raising the tracks and trenching the road to go beneath the tracks. By changing these four crossings, the HSR would have longer uninterrupted sections for higher speed travel. Presumably a key factor for both raising the tracks and lowering the road is to minimize how much property would have to be seized through eminent domain … clover leaf interchanges require space (Oregon Ave underpass)
The third phase creates a stretch of track free of grade crossings from the southern half of Palo Alto all of the way to San Jose. Completion is expected in the late 2020s. Again the grade separation is achieved by combining raising the tracks and trenching the roadway.
Homeowners currently living near the tracks have been hoping better solutions would be found. Unfortunately the blog is probably quite close to what will happen.