Hi Ruby--I'm sure you are somewhat familiar with Bernal Heights and its different areas, given that you're interested in purchasing a home there. The properties on the south side of Cortland tend to be less expensive, as they're close to the freeway and the housing projects. That being said, I've successfully sold homes in all areas of Bernal (including on Crescent, close to Mission), and the desirability of the houses have depended on additional factors besides location.
Another neighborhood you might consider is Excelsior, which is just down the road from Bernal. Great values there, and a lot of first-time home buyers are turning to the area for the space they need.
Feel free to check out my blog, Inside San Francisco Real Estate, for coverage on Bernal, Excelsior, and a lot of other neighborhoods. I live on the Noe/Mission border and predominantly sell homes in the south part of SF.