I personally don't see any problem with Caltrain. It's relatively reliable and goes often enough. The only thing that's missing is free wi-fi, but I think they plan to put it in there eventually.
The problem is nobody uses it. Metro North serves a region with maybe 2-3 million people (depending on how many people in Connecticut you consider part of the service area), and has a ridership of 300,000 per day. Cal Train serves a region that's at least as large, but has 40,000 riders a day.
I personally don't see any problem with Caltrain. It's relatively reliable and goes often enough. The only thing that's missing is free wi-fi, but I think they plan to put it in there eventually.