The big question is whether patents work for the benefit of society
The theory of why patents should work for the good of society is well known. But the empirical question (ie whether the benefits actually materialise) is much less studied.
There is a body of evidence that suggests the benefits are not seen in reality and that most intellectual property restrictions have been bad for us, at least since the early patents on the steam engine which held back progress for decades. There is a good summary of the arguments and the evidence on the skeptics stackexchange site here: http://skeptics.stackexchange.com/questions/6647/do-patents-boost-innovation
(I wrote one of the answers summarising the book-length case from Against Intellectual Monopoly available as a pdf for free here: http://www.dklevine.com/general/intellectual/againstfinal.htm )
In summary: the benefits of patents are not as obvious as the normal arguments for them would lead you to expect.