Marin to San Francisco is an interesting example because Marin Transit has next to no idea what the fuck they're doing. My experience over a few decades is that getting to/from Marin-SF on public transit typically takes 2-3 hours depending on how far away from downtown SF and 3rd/Hetherton you're going. If the delta between driving and taking the bus is only 15 minutes you either get stuck in awful traffic or live very close to a 30/70/101 bus stop.
Grievances:
The 101 is a great idea, a limited stop bus from SF to Santa Rosa that can basically camp out in the carpool lane. Except that in their infinite wisdom, Marin Transit doesn't actually time transfers in San Rafael. Unless you live within walking distance of a 101 stop you're often just wasting your time.
Real-time predictions sound great, except that Marin Transit is pairing with the Transit app. For a while was providing completely fabricated predictions. Sorry, you're only going to leave me stranded in the middle of the night once before I dump your app. NextBus has its share of problems too, but the difference is that Muni runs such frequent service you're more concerned with predictions and headways than with schedules. Marin Transit runs such sparse service that you absolutely need to adhere to a schedule.
A zone based fare system sounds reasonable to most people. Unfortunately Marin Transit is not set up to refund overcharges when you can't tag off as you exit the vehicle (e.g. when their own equipment doesn't work). Zone based fares also complicate cash payments wildly slowing down the boarding process. Unfortunately Marin Transit refuses to let people alight from or board with RFID payment via the rear doors slowing down the whole process even more.
The Golden Gate Bridge District (one of the folks Marin Transit contracts out to) leased another ferry knowing that the engine wasn't compliant with California emissions requirements. In their due diligence they never realized that it is physically impossible to retrofit a compliant engine into that heap. It's still not in revenue service.
Historically there have been very few feeder routes because people tend to like to keep the poors out (Tiburon is notoriously bad). So to get from Marin to San Francisco you're often walking all the way out to the highway, sometimes along roads with no sidewalks (I'm looking at you Sleepy Hollow). SMART also suffers because of this. Getting to a SMART station can easily be a 30 minute walk along a route with no bus service.
That said, things don't actually have to be this way. But Marin likes its privilege[1].
1: https://www.reddit.com/r/Marin/comments/coz8ro/smart_train_s...