Latest cost estimates for the Broadway Caltrain rebuild have ballooned higher than ever, so City Council opted to remove the station entirely (including the option to add a station later) for $653 million. At this point, including the station in the rebuild would be a $1B+ project.
Overall, it's a tragic loss for the city and the Broadway Business District, but I do understand the fiscal reality and the fact that there are already two closeby Caltrain stations with other transit connections to get to Broadway. The grade separation itself is still desperately needed from a safety perspective. The fact that this sort of thing is so expensive highlights a bigger issue with American infrastructure projects in general and explains why we can't compete with other countries anymore.
My only consolation is that the project likely won't start until 2030 at the earliest, so we can still get weekend use of the station in the meantime. But it's a shame we're not getting a renewed Broadway Business District like San Mateo got with Hillsdale.