It's supposed to get somewhat better with electrification, since they'll be able to run more trains so we'll have more frequent service. I agree though that we need good transit on top of Caltrain, and it should be separated-grade.
I'd like to see Bart or similar all the way down the el camino and encourage high density housing and offices. Create a nice long urban canyon with good transit. People could bike a few blocks off the stations.
I don't have details, but apparently BART was originally drawn up to encircle the South Bay but that was torpedoed by the local communities on the peninsula just like high speed rail to LA. It's sort of crazy making to think about how much better BART would be compared to the apocalyptic, earthquake-inducing rumbling and dinging bells of Caltrain with at-grade crossings and monthly deaths (sometimes intentional, sometimes not).