This thread made me laugh. I played Rancho San Joaquin a handful of times when I first started getting into golf seriously. I hated the course with a white hot passion due to all of the issues mentioned above. Hardpan fairway lies? Check. Slow & inconsistent greens? Check. Slow pace of play? You bet! Finally, I just swore off the course entirely and didn't play there at all for about 3-4 years.
But earlier this summer, some work colleagues who are fairly new to the game suggested a golf outing and I couldn't think of a better place to bring a couple of beginners than good ole' Rancho San Joaquin. Wouldn't you know it, after about 4 tall boys, I end up shooting the best of round of my life - a 76. I guess I don't feel so negatively about the course now, but it's certainly not because of any improved conditions!
I would echo the comments above that Mile Square is a really good value for the quality of course. The two tracks - Classic and Players - criss cross with one another, but somehow manage to maintain a distinctively separate feel. The greens on both are usually in pretty good shape, and if you are able to score an early twilight round midweek, you can usually finish your round in under 4.5 hours.
Costa Mesa is a step below Mile Square in terms of quality - you aren't going to find a more generic muni in all of OC - but it does the trick in a pinch. I would definitely play there ahead of RSJ. I used to love Arroyo Trabuco, but I haven't played there in awhile. I'm sorry to hear about some of the challenges they have had with their greens.
If you don't mind spending a few extra bucks, Coyote Hills in Fullerton is a tight challenging course and is always well maintained.