Right. The transit agency is spending about $200M for the Clipper 2.0 project, so why not implement more future proof solution?
Bay Area is Silicon Valley. If there's a metropolitan area in the US that would adopt technology, this is it. The transit agency is being very obtuse to embrace a proprietary technology (using a vendor with questionable ethical standards) without modernizing outdated fare system.
Judging by other Cubic rollouts, it would be pretty simple to add Open-Loop payments at the flip of a switch, or maybe the addition of a payment module at the back end of things. The card readers etc already would support it, just won't do anything when you try to tap a regular credit card. This would make the cubic system already future proof.
I think the real reason they don't want to implement open-loop payments, is the 1-3% Visa/MasterCard/Amex/Discover fees they'd have to pay every time someone boards a bus.
A virtual Clipper Card inside of Apple Pay gives everyone what they're looking for in a way, MTC won't have to pay those transaction fees, and people still get to pay with their phones. OMNY, Hop & Ventra will also allow virtual "passes" on the phone, but these cities also allow you to just tap a regular credit card as well.
As for switching Vendors, lets see how the San Diego project rolls out. It means new everything, fareboxes on the bus (Which Muni DID just replace, so hoping they can get more life out of those), card readers at the train station platforms, CAD/AVL integrations (Muni just spent a lot of money with Xerox for these as well, which is designed to also interface with the Cubic system), in the case of Muni/BART, new fare gates, which would make it much more expensive and wasteful than just going with the same vendor.