both are strong programs in my opinion.
Scripps Mercy always gets a little shortchanged when people talk about them because it's a community hospital program. But they have a very outstanding program director, and everything is geared toward resident education. No scutwork here; outstanding computer system. Very happy residents; and something like q12 overnight call. For those in the know, it's regarded as a very strong program. They might place fewer people in fellowships though, only for the reason that people who go there are possibly looking more toward primary care.
Scripps Green is another outstanding program; it's also technically a community hospital program, but it has the well-renowned Scripps Research Institute next door. It's a smaller program, which might turn off some people, but that translates into more personal attention to your education, and their attendings considering you more as a colleague as opposed to a puny resident. Part of the hospital looks retro 70's but the outpatient clinic is nice. The locations is amazing too...overlooking a golf course overlooking the Pacific. The disadvantage of the program is a antiquated computer system and no radiological images on computer: very dark ages. I've heard they've been promising one for awhile but haven't delivered. Otherwise resident here seemed quite happy.