Microsoft and Samsung, the world's number two mobile manufacturer behind Apple, announced a major patent licensing deal on Wednesday. The agreement means that any time Samsung sells a Google Android-powered phone or tablet, they will pay a royalty to Microsoft. The joint press release also says that Samsung has also agreed "to cooperate in the development and marketing of Windows Phone," which involves paying Microsoft a licensing fee for their own mobile OS. On the surface, it may make it look like Samsung will have an easier time making Android phones going forward. But it really demonstrates just how much vulnerability the Android platform has in Silcon Valley's patent wars. And just how little protection Google has to offer its partners from infringement lawsuits.

Samsung and other mobile manufacturers are faced with a growing list of reasons to abandon Android. The new deal comes hot on the heels of Google's announcing their intentions to acquire Motorola Mobility. One is that Google moving into the hardware business with its acquisition of Motorola. But Android-phonemakers Samsung and HTC are also currently battling dozens of lawsuits--most of them filed by Apple--over software patents. Google has admitted that their Motorola bid was largely an effort to build out their patent portfolio in order to defend themselves and their partners against these kinds of suits. Though as Jordon Cook at TechCrunch points out:

If Samsung had faith that the Googorola deal would be beneficial to Android, there would be no need to sign on the dotted line until the acquisition was closed.… As far as Apple and Samsung are concerned, this won't do much to change the state of affairs. Samsung can't suddenly begin fighting Apple with Microsoft patents. The deal only allows Samsung to build products or practice technology covered in Microsoft's patents moving forward. However, it does make plain how Samsung perceives Android at the moment--in peril.

Meanwhile, Microsoft looks diplomatic in their attempts to spin the partnership as a goodwill gesture towards Google. In a blog post coinciding with the Samsung announcement, Microsoft's chief lawyers noted Google's complaining "about the potential impact of patents on Android and software innovation" and heralded patent licensing agreements as a way "to address intellectual property issues in a responsible manner." They asked, "If industry leaders such as Samsung and HTC can enter into these agreements, doesn't this provide a clear path forward?"

This brings us to another item on the list of reasons to abandon Android: rising costs. Google has always billed Android as a free, open source operating system, but Android's hidden costs are actually pretty significant. Besides the cost of potential patent infringement lawsuits, Google offers little technical support for Android partners, leaving companies like Samsung and HTC to spend their resources on development and maintenance. Patent licensing deals provide manufacturers with some insulation from infringement lawsuits, but it also means they're essentially paying a fee to use the Android operating system.

Not so coincidentally, Microsoft offers an Android alternative. Their Windows Phone operating system is not free--they charge manufacturers a licensing fee of about $15 per unit--but back-of-the napkin math suggests that figure's cheaper than Android's hidden cost also provide options that Android doesn't like deeper, easier customization and automated testing that makes it easier to implement the software. As Microsoft announced in their press release, Samsung and Microsoft will cooperate on building a Windows Phone device, but cooperating with Microsoft doesn't necessarily mean that Samsung will build a Windows Phone. If precedent is any guide, it's likely. Almost exactly a year after they inked a similar patent deal with Microsoft, HTC rolled out their line of Windows phones this month. They're getting great reviews.

Inevitably, companies like Samsung and HTC could abandon Android in order to build their own operating system. HP's webOS is also for sale. Who knows, but Dan Ravicher, head of the Public Patent Foundation, says that Microsoft thrives in the vacuum of certainty. "Microsoft is up to its usual FUD [fear, uncertainty and doubt]," Ravitch told CNET. "This is not a new phenomenon. MS doesn't make good products any more, so all it can do is try to leech off those that do."