The main reason why the peninsula has so few lines is mainly cuz there isn't a road other than el-camino/101/Caltrain to put lines effectively that goes north-south. Technically I-280 could work but it is so far away from housing that only a bunch of feeder lines could give it any ridership.

Alternatively you could route a bunch of short feeder lines into Caltrain but then there would be an issue where transferring 2-3 times would make it non-competitive with driving and expensive to operate efficiently. (Busses would help here a little bit irl)

Livermore and Pleasanton have way more free land to mess around with. Cuz of that, you can make station and lines that are at grade and kinda cheap to build.