Is it better or worse regarding those 5 items?

Many people regard SF as above average in water and bread. Water comes from Hetch Hetchy [1] and many of the regions best bakers are in SF, such as Acme [2].

[1] https://en.wikipedia.org/wiki/San_Francisco_Public_Utilities...

[2] http://acmebread.com/

How is SF considered above average in bread? Is it due to all the golden wheat fields rolling through Silicon Valley?

I jest of course, but seriously, all regions have a ton of variety of breads and bakeries. Even tiny podunk towns you wouldn't know existed...

A long history with sourdough (hence Lactobacillus sanfranciscensis, even though it didn't originate in California), and more recently a strong network of bakers and bakeries branching out from Chez Panisse starting in the 70's as noted in another comment.

Probably has to do with san francisco sourdough.

Far, far, better for bread and cheese at least. Which I suspect means you haven't found where those are? (Cheeseboard in Berkeley, Cowgirl Creamery in the Ferry Building, Acme bread, Tartine as previously mentioned - some of these closed at the moment of course)

[I'm a cheese and bread snob from Switzerland FWIW - I could be somewhat convinced that the wholewheat bread choices are not perfect though]

Do you know of a good pumpernickel here?