I am not a profesional writer, but I will try and help as much as a can.
Can two cities, located within the same region of California share similar qualities, yet have distinct differences?
You do not need a comma after cities.
have a higher rate of automobile traffic
I would reword this somehow. Firstly, I do not think you need to say "automobile traffic." It just seems to me that you are talking about a city and most people will know what kind of traffic you are refering to. Also, "higher rate" does not sound right in this sentence either. Maybe you could say "higher rate of automible accidents" or "a higher volume of traffic."
Although San Diego does not have as great of a problem with traffic and statistically has a lower crime rate than Los Angeles, both cities, nonetheless have a presence of these negative issues
You need a comma after Although. I would also do a little rewording to this sentence. It is a little long and choppy. Maybe you could say, "San Diego has fewer problems with traffic and crime than Las Angeles, but both cities have a significant pressence of these negative issues.
For example, I find that the locals of San Diego are more likely to say hello to a stranger than in Los Angeles where a local is more apt to ignore someone and not even make any eye contact.
This is another long and hard to follow sentence. The end of the sentence sounds repeptitive. Avoiding eye contact and ignoring someone are virtually the same. I would reword it like this: "For example, the locals of San Diego are more likely to be friendly to a stranger, whereas, the locals of Los Angeles are more apt to ignore a stranger.
Although there are only separated by approximately 130 miles,
"Although they..."
Even though Los Angeles may have a greater point of interest index and is known more worldwide than San Diego and has higher rate of pay, the hustle and bustle and aggressiveness of the city outweighs its positive attributes.
Very chopy and hard to follow sentence. It feels like you are saying "and" way to many times. I would also reword this one as well.
They don't call it American's Finest City for nothing!
This is probably being a little to picky, but I would say "do not" instead of "don't" in an essay.
It looks like you are off to a great start. I think you will have a great paper if you do a little touching up. Hopefully, some of this advice will help you out.