SF literally burned and regrew as well: http://en.wikipedia.org/wiki/1906_San_Francisco_earthquake

Yeah, if you're looking for it, you can see the phoenix motif all around San Francisco, not just on flags. It's the symbol of the city.. a city risen from its ashes. I quite like it actually, though I agree the actual flag is not the greatest design. He didnt mention it but the gold border is a reference to the gold rush roots of the city, if that wasnt apparent.

I dont think the flag is that hard to find.. it's flying over most government buildings at least. Though I may be inclined to notice these things since I could name the cities for a few of flags on his "bad flag" slide by sight.

The LA flag fits LA pretty well, what would you do differently?

This proposal's not bad: http://imgur.com/a/h70HJ

Hmm, I prefer the south-west color scheme of the original, though the star isn't too bad.