This redesign incorporates two of the worst design trends today: very low contrast text and gratuitously, obnoxiously large fixed headers.
I dislike fixed headers on any non-phone/tablet UI because almost all laptop and desktop screens are widescreen. Fixed position elements on the sides of the screen make much more sense, although poor implementations are very unpleasant and can create a jarring parallax effect. Unfortunately, fixed elements on the sides are soooo MySpace and have fallen out fashion, and many sites waste most of the space on the sides. The header in the redesign in obscenely large and the new page shows me less results at a time.
I have young and healthy eyes with 20/20 vision. Even so, when I use my laptop for coding and reading text, I turn the brightness down because it is easier on my eyes and does not give me headaches. I believe that the best practice is to make text #000 on a white background or very light background (like news.yc does), and to let users adjust the brightness of their display if this is uncomfortable. There have been assertions by that lighter text with white is better (and unfortunately this is the latest and laziest design trend), but I have seen no formal evidence of this and believe that this is mostly a combination of overbright display screens and poor text rendering by OSes and browsers. If you turn the brightness of your screen down, you solve the "too much contrast" problem (if it ever truly existed) and can tell when any text isn't #000. For me, DuckDuckgo's current snippet display color is to light at #333, and ridiculous at #595959. If I set the brightness of my laptop to the maximum setting, the snippet text is more tolerable but still uncomfortable.
I dislike the neo-flat, iOS-like buttons, but they don't really make the site any harder to use. I find that neo-flat buttons are almost have an underlying hypocrisy. The idea behind the flat painting movement is that you can discern what was called "optical depth" without using traditional perspective to mimic the depth you see with stereoscopic vision. The neo-flat movement is based on the idea that you don't need to underline hyperlinks or add perspective based shadows and gradients to distinguish what a button is because you can just use colors alone or make everything a link. If this were really true, then you wouldn't need to make the neo-flat buttons change colors when you mouse over them, because it should be obvious that they are links. You can see similar hypocrisy in Google's A/B testing of non-centered labels in certain neo-flat buttons on their websites (especially YouTube).
Edit: I rewrote the first sentence of the third paragraph to make it more clear.