Edit: One thing they could fix, easily; unified, visitor accessible, payment system. And more realtime bus information. Those are simple things that they could borrow off any decent-sized European city.
Further edit: looks like the Clipper card is easier to get than I thought. Googled before I went, but must have gotten outdated information.
These do exist: purchasing fares via the Muni app is pretty straightforward and services like nextmuni.com and similar apps can tell you when the next bus is coming.
Frequency is definitely subpar though. When I first came to SF, I was supposed to meet with a job interviewer for dinner in a place at mission. The subway train took 30 minutes to show up!
I'm not sure how most visitors to the bay get in but two desks at SFO and OAK across from baggage claim seem like a good start to implement the same kind of solution.