The SF Bay Area really did the right thing here.
No, no they really didn't. They spent millions rebranding it, there is (was?) a huge lag between adding value and posting the value depending on how you added value. The original card readers were incredibly unreliable, and because Clipper/TransLink did absolutely nothing to unify* the fare structure across the twenty-four different systems you could be set up for a nasty encounter with a pop cop because you couldn't tag on or get charged the max fare when you can't tap off. Been there, done that.
BART did their best to make a fantastic mess too and, at least according to their web site, they still only sell paper tickets at SFO. For whatever reason the three other vendors at SFO do sell plastic cards. Because three additional vendors isn't confusing at all.
* Some systems are flat rate (Muni, Golden Gate Ferry, VTA), some are zone based (Caltrain, Golden Gate Transit, Marin Transit), and some are distance based (BART), SamTrans has a flat rate depending on the type of bus you're on. Some systems are proof of payment (Muni), some use turnstiles (BART), some are partially proof-of-payment (AC Transit). And some (AC Transit, Muni) still maintain their own proprietary mobile payment systems. It's still a fucking mess.