The trend of using ultrathin fonts everywhere will be short-lived and date interfaces quickly. It's a trend inspired totally by the mere fact that high dpi displays can render them without pixelated artifacts, and not because they make sense for design or readability on a fundamental level.
Thin weight type has uses in good design, but the way it's being applied ad nauseum today is a gimmick.
Modern fonts have been frequently thin before the invention of retina screens.
The overuse of thin fonts might look dated in the future, but I don't agree that this trend is totally inspired by retina screens. If anything, I think Serif fonts have seen the greatest resurgence on web due to Retina screens. High DPI screens will impact our perception of all fonts, just as sans serif grew in popularity on lower dpi screens causing their perception to be more modern and technological.
In general typography as a whole has become much more interesting on retina screens. So yes, fonts look better now than ever before so don't cheat by using superthin because its trendy.
Sans-serif typefaces were historically perceived as more modern than their serif counterparts. The simplicity and lack of letterform "decorations" (which serifs are) suggests a character of precision and rejection of legacy and "old ways". This has been the case ever since Swiss designers started using Helvetica and related typefaces set in clear, grid-based designs with modern color choices. So the modern character of sans-serifs dates far before computers and computer displays.
The screenshots on github use the thin variant of San Francisco - the equivalent to the current Helvetica Neue would be regular San Francisco. I also suspect they use the "Display" instead of "Text" version, which makes the kerning look strange.
San Francisco seems to work best at (very) small sizes, where Helvetica breaks. It proves further that Apple thinks of each screen size as a distinct UI - clearly the biggest difference with Google's approach to UI. Off topic: the 2 screen sizes for Watch show they don't want accidental developers for this platform, only fully committed ones.
I do find Helvetica works better on my Mac screen than SF (I tested in Mail.app).
iOS hasn't used ultrathin Helvetica since its early betas, and I'm not aware of anywhere substantial in Yosemite that uses ultrathin. I believe mostly everything is regular Helvetica.
This reminds me of Computer Modern (the companion default font for TeX) and what is wrong with it. It's even a reasonable explanation of why it is that way - new technology.
Thin weight type has uses in good design, but the way it's being applied ad nauseum today is a gimmick.