The Draft Program EIR/EIS for ACE's planned expansion is supposed to come out this fall. They have some good ideas and options in there, including smaller near term improvements. Niles Junction is really the critical chokepoint for ACE, Capitol Corridors, and UP.
One of the things Alameda County has been trying to push on ACE is an emphasis on extending BART to Livermore and doing a direct connection to ACE. They're throwing lots of different alternatives for this in the EIR/EIS. BART doesn't want anything to do with the extension to Livermore, so Alameda is trying to pass legislation to create a new JPA to take over the process similar to VTA's current extension, the Gold Line, etc.
Nifty PowerPoint:
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