The patent system is probably flawed (IANAL), but companies do need to have a way to defend their innovations. Apple did re-invent the smart phone in 07, and has been the design leader since then.
Android has followed in their footsteps - witness the design shift from their pre-iphone roadmap which consisted of blackberry-look-alike designs.
Further, there have been no bold re-imaginings of the smartphone in Android-land (sorry, a better notification system doesn't really qualify). They are taking Apple's innovations and applying a different business model to achieve success.
Google and Apple are both amazing companies, but I have a hard time finding fault with Apple's decision to sue Google's partners. If the tables were turned, and Google came out with an Android phone first, I would support Google suing Apple for the same reasons.