Time in San Jose depends on what kind of traveler you are. SJ is certainly not what most people think of when they think of Costa Rica. There's plenty to do in SJ -- I live in SJ and I never get bored -- but it's a city. There are no beaches, volcanoes, rainforests, and certainly not much wildlife in the city. Lots of culture, events, nightlife, people-watching, etc.
La Fortuna to Manuel Antonio is at least a 5 hour drive... or a 25 minute flight.