Which would be better???

As to those 2 places specifically:
San Isidro is a farm town. I imagine it's grown quite a bit from when I used to spend time there, 18 years ago, but I also imagine it's not that different in that it's a slower paced town, not a lot of traffic, not a lot to do, yet very tranquil for a town of its size. Just a nice quiet traditional Costa Rica town whose economy is largely based on the farms around it.

San Jose on the other hand is a big city like any big city that has a lot of traffic, smog and people. The surrounding areas are nicer, less "big city-ish" for sure, but still have a "city" feel to them.

I would point out also that - without having statistics to quote from - San Jose' and surrounding areas surely have more crime than San Isidro.

Personally I much prefer San Isidro, and even moreso the areas surrounding it. It's only 45 min or so from the beach and some nice beaches just a little further out.

Originally I wanted to live in an area between San Isidro and the beach but a) the property values went sky high out that way; b) it's 3 hours from San Jose on a very windy and somewhat dangerous highway; and c) it rains a lot more than some other areas. I chose San Ramon because it's closer to San Jose' for medical care and things, the airport is closer, and it's a nice medium sized town with a kind of small town atmosphere and also has a hospital and doctors and such.

Like the other posts said, though, you just have to go and figure out what YOU like, as everyone is different. Some people prefer to live near San Jose' because there's a lot to do, more people to meet and so on. I am one of the few people who LIKE visiting San Jose' - I think it's fun and interesting. But I'd say the majority of expats hate it. And I wouldn't want to LIVE there or too near it.