Dammit, I am so sick of the word "innovation", Fnord. Innovation is not progress or improvement. Innovation is simply change. You can't stiffle change. Maybe if "alternative" software developers were less interested in copying everything Microsoft and Apple did, and really DID innovate new, bold ideas, they wouldn't bitch so much about patents.
You got a problem with the MP3 patent? Make something else! Your MP3 player won't play the new, patent-free format? Tough. The problem is that people are too damn lazy to protest and boycott.