One option on the Fremont-to-Merced route that avoids the bus would be to take BART from Fremont - Richmond (~1 hour), and make the quick transfer to the Richmond Amtrak station. This adds an extra 20-30 minutes to the trip, but you're getting the San Joaquin train earlier in the route, so the chances for it to be delayed are less. Plus, then you can avoid the congested 580 traffic and spend more time on the train & less on the bus, always a plus.

An alternative would have been for UC to put the campus somewhere easier to get to, but that subject was talked to death after Merced was announced.

-Hayden