It seems that, on my computer, Yosemite Preview (and also Skim) display pdf fonts very differently than Maverick Preview (and also Yosemite Safari). There was no such problem in Maveric and the checkbox "Use LCD font smoothing when available" is checked. Moreover, the issue happens both with an Imac and an external display. Left is Safari, Right is Preview.
I have looked on the Internet but I could not find anyone with the same issue. Would someone know where does the problem come from? If anyone thinks of a solution less drastic than a clean installation, I'd be glad to hear it.