There's plenty of evidence if you actually look for it, rather than make up your mind and never seek to challenge your beliefs. Allow me to share:

A paper (Bessen, Maskin - 1999) that argues patents may hinder innovation[1]. Abstract:

"How could such industries as software, semiconductors, and computers have been so innovative despite historically weak patent protection? We argue that if innovation is both sequential and complementary—as it certainly has been in those industries—competition can increase firms’ future profits thus offsetting short-term dissipation of rents. A simple model also shows that in such a dynamic industry, patent protection may reduce overall innovation and social welfare. The natural experiment that occurred when patent protection was extended to software in the 1980's provides a test of this model. Standard arguments would predict that R&D intensity and productivity should have increased among patenting firms.
Consistent with our model, however, these increases did not occur. Other evidence supporting our model includes a distinctive pattern of cross-licensing in these industries and a positive relationship between rates of innovation and firm entry."

Here's another paper on the same topic (Bessen, Hunt - 2004). Abstract:

"U.S. legal changes have made it easier to obtain patents on inventions that use software.
Software patents have grown rapidly and now comprise 15 percent of all patents. They
are acquired primarily by large manufacturing firms in industries known for strategic
patenting; only 5 percent belong to software publishers. The very large increase in
software patent propensity over time is not adequately explained by changes in R&D
investments, employment of computer programmers, or productivity growth. The residual
increase in patent propensity is consistent with a sizeable rise in the cost effectiveness of
software patents during the 1990s. We find evidence that software patents substitute for
R&D at the firm level; they are associated with lower R&D intensity. This result occurs
primarily in industries known for strategic patenting and is difficult to reconcile with the
traditional incentive theory of patents."

An abstract from another paper (Bessen, Meuer, Ford - 2011) showing that lawsuits by non-practicing entities have cost the tech industry $500 billion over a 20 year period (from 1990 to 2010), with almost none of it going to the inventors:

"In the past, non-practicing entities (NPEs) - firms that license patents without producing goods - have facilitated technology markets and increased rents for small inventors. Is this also true for today’s NPEs? Or are they “patent trolls” who opportunistically litigate over software patents with unpredictable boundaries? Using stock market event studies around patent lawsuit filings, we find that NPE lawsuits are associated with half a trillion dollars of lost wealth to defendants from 1990 through 2010, mostly from technology companies. Moreover, very little of this loss represents a transfer to small inventors. Instead, it implies reduced innovation incentives."

And an abstract from yet another paper (Feldman, Lemley - 2015) showing that patent licenses do not drive innovation:

"A commonly offered justification for patent trolls or non-practicing entities (NPEs) is that they serve as a middleman, facilitating innovation and bringing new technology from inventors to those who can implement it. We survey those involved in patent licensing to see how often patent license demands actually led to innovation or technology transfer. We find that very few patent license demands actually lead to new innovation; most simply involve payment for the freedom to keep doing what the licensee was already doing. Surprisingly, this is true not only of NPE licenses but even of licenses from product-producing companies and universities. Our results cast significant doubt on one common justification for patent trolls."

And finally, a paper (Johnson - 2011) that argues, using recent advances in relevant fields, that the fundamental belief that external incentives such as copyrights and patents are necessary for innovation is fundamentally wrong:

"The enterprise of intellectual property law has long been based on the premise that external incentives – such as copyrights and patents – are necessary to get people to produce artistic works and technological innovations. This article argues that this foundational belief is wrong. Using recent advances in behavioral economics, psychology, and business-management studies, along with empirical investigations of industry, it is now possible to construct a compelling case that the incentive theory, as a general matter, is mistaken, and that natural and intrinsic motivations will cause technology and the arts to flourish even in the absence of externally supplied rewards. The result is that intellectual property law itself needs a fundamental rethinking."

[1]: http://www.researchoninnovation.org/patent.pdf
[2]: http://www.researchoninnovation.org/swpat.pdf
[3]: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1930272
[4]: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=2565292
[5]: http://papers.ssrn.com/sol3/papers.cfm?abstract_id=1746343

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In fact, the only real evidence we have that patents may be a net positive is in biotech, and that's due to the extremely time-consuming and massively expensive process of R&D in that field. In every other field, we either have no evidence that patents drive innovation, or we have evidence that they hinder it.