Since I got hit by CalTrain, it appears that just possibly CalTrain has stopped routinely running trains on the wrong track past the Santa Clara station. I haven't seen a Southbound train pass on the far track in quite some time now. It used to be that the trains had a 50:50 chance of being on opposite tracks at the 8:00 AM hour. That's a good thing. It will improve safety at Santa Clara, but not as much as it needs.
Things should still be improved. I believe Santa Clara may still be one of the least safe stations left on the CalTrain line. Most stations either have two outside platforms with grade separated ingress/egress (that is, a tunnel or a pedestrian overcrossing), a single shared platform between the tracks with grade-separated ingress/egress, or two outside platforms with crossing gates protecting the tracks.
In the latter case, the crossing gates serve an extra purpose which they perhaps were not designed to do, but do anyway: they warn people in the station about an approaching train.
This morning, I got to Santa Clara a little bit later than usual, and presumed that I missed the Southbound express that normally roars through at about 8:20. That train was a little bit late. I was standing on the platform (a safe distance from the tracks, of course), when I heard a train whistle from the North and turned around to see the Southbound express only a couple seconds away from the station flying at 79 mi/hr. Part of the reason this is such a surprise is that just North of the station, the tracks curve to the left a bit, which means that people in the station can't watch for trains approaching, like they can from the South. And, of course, the Southbound trains approach the tracks closest to the platform.
This, in my view, is a dangerous setup.
Now, this isn't really an issue in and of itself. You could argue that people should presume that a train can fly past at any moment, and should give the tracks the respect they deserve. But just saying that isn't going to make people do the right thing.
The damning thing is that this would be really, really easy to fix. All that needs to happen is pouring a concrete slab to act as a Northbound platform on the far side of that track, putting a fence down the middle between the two tracks, and add a pair of crossing gates at either end. I'd expect to pay, what? $10,000 to have that work done? Even if you triple that (because the government is involved), that's $30K. The crossing gates will keep people off the tracks when trains are approaching, but more importantly, they'll warn people on the platform that a train is approaching, particularly from the North since otherwise there is no warning at all. Governments piss away bigger sums of money daily on dumber stuff than that.
Sometime in the next 20 years, BART is going to put a station in and the whole place will get gentrified. But the BART station is hardly going to invalidate the idea of fixing the safety issues now. It's not as if they're going to move the CalTrain station anywhere else.
UPDATE: Thanks to Dan in the comments, and google, I've discovered this announcement of CalTrain's plans for improving the Santa Clara station. Interestingly, the plans include a tunnel rather than gated crossings, and (combining Dan's comment) it would appear that the new outside platform is actually going to serve both the current Northbound CalTrain track, but also the next track East of that, which will make it easier (I won't say possible since there are switches that would route trains from the Northbound CalTrain track to the next track to the East, which branches off in the Fremont-bound direction) to allow Capital Corridor and ACE trains to once again stop at Santa Clara.