I agree with that. San Francisco seems optimal for button captions, app names and other more unique, short pieces of texts, but seems sub-optimal for running text.
Helvetica is a typeface designed for signage, headings, posters, corporate logos, and the like. For body copy, it’s terrible, because it has a strong boxy/griddy quality to it, many similar looking letters, and proportions which make letter shapes hard to see at small sizes.
For my taste San Francisco looks a bit too blocky due to the flattened curves along the vertical axis. It's not bad, but I like Google's Roboto typeface, for example, better.