I am still working out how to best use pdf annotation software, so I readily admit that some problems that I have with all of the applications I've tried may not be problems at all. Problems such as writing notes - the equivalent of writing in the margins on a hard copy. Skim, PDFpenPro etc. all have these anchored notes that are nothing short of inconvenient. They're more like Post-its/stickies and just like those big yellow eyesores, they get in the way of the text. You can sort of hide them, but the little anchor is still in the way. The ideal for me would be something like the reviewing function in Word, but as a separate layer so I don't accidentally edit, delete, or simply select a note when I'm working from the document. Also, a nice looking font and layout preset for notes would be welcome.
But Skim specifically. Overall, it's a great little program. I learned about it on an academic blog in a post about the writer's workflow. On the whole, I'd agree that it fits an academic workflow quite well.
My only major gripe is that it does not yet, years after Lion, have fullscreen mode. This was actually not too bad on 10.7 and 10.8, but now Apple has finally fixed the multi-monitor bug, it's time Skim has fullscreen mode. Why is fullscreen mode so important? Partly because of the slightly illogical way Apple has set up Spaces. If, say, you have several documents open in Skim in its current full screen setting (with each document open on a different Space), and then open another application, that application may open on top of an open skim document. Not the end of the world, but rather annoying.
My other little gripe is that Skim will not restore windows when it is reopened. There is an option to "Reopen last open files at startup" but this seems to do absolutely nothing.
Still, this is free software and it is, in my opinion, much better than PDFpenPro. Hats off to the developer for the work put into this application. A lot of free software is kind of like a generic drug - almost as good as the real thing. Skim, however, is better than the paid applications available.