Amazon took another step toward co-opting Google’s mobile operating system this week when it launched the beta version of an API enabling Android developers to place Amazon-based ads in their apps. The move will enable developers to sell in-app ad inventory through Amazon, placing those ads in apps downloaded through Amazon’s Appstore on any device – not just the Kindle line of tablets. The Verge points out that Amazon is promising “competitive CPMs,” indicating it aims to outperform ads delivered through Google, and notes that the online retailer may be looking to become a full-blown ad network alongside Google, Millennial Media and many others.

And Amazon isn’t the only mobile player looking to use Android as a weapon against the company that built it: Samsung is aggressively pursuing the mobile enterprise market with SAFE (Samsung for Enterprise), which aims to deliver corporate-grade devices and services on the Android platform. Samsung also is targeting consumers with an intriguing new partnership with Electronic Arts to bring edgy mobile games to market through Samsung’s existing app store.

The shortcomings of Google’s ecosystem

This emerging co-opetition is possible, of course, because Android is an open source platform that anyone can make their own. But Google’s ecosystem has some flaws that Amazon and Samsung hope to capitalize on: Google Play is an overwhelming and confusing morass of hundreds of thousands of apps, many of which are knockoffs or simply garbage. Discovering the best apps – as opposed to the highest-rated ones – is sometimes impossible within the store itself. As I’ve long argued, that has created an opportunity for a curated store of Android apps that culls the best, most innovative offerings and eschews the also-rans.

Also, while the vast diversity of Android devices has fueled its astounding worldwide growth, its inevitable fragmentation has caused headaches for consumers and stifled its penetration into the corporate world. And the combination of Android’s immense popularity and its freely available code has made the platform a bigger target than Windows for malware, according to one recent report. It’s no surprise, then, that Android remains a substantial concern for the IT professionals who often are charged with supporting it.

Avoiding the slumlord scenario

The new initiatives from Amazon and Samsung threaten to relegate Google to a second-tier player in the world of Android, the Wal-Mart of the operating system it created and shared with its partners. That’s not such a horrible fate – Google will always be the default distributor of Android apps, and the sheer worldwide footprint of the platform is more than enough to ensure the company impressive mobile app and advertising for years to come. But it would be a huge lost opportunity for Google to dominate the very top of the Android food chain.

There are a few ways Google could take on Amazon and Samsung directly, though, while it manages the overall world of Android as well as it can. As I argued almost a year ago, Google could build a kind of uber-Android ecosystem that offers only the best titles from Google Play, rebranding the storefront to convey its value. That storefront should continue to build on its tools for the enterprise like the distribution channel for custom-built business apps that it launched a few months ago. And while it will take a while to flush Motorola’s product pipeline, it must hastily work with its new manufacturing business to develop gadgets that are more tightly integrated with Android than any other hardware vendor can build. (Google will also control the deployment of Android upgrades to those gadgets, minimizing fragmentation problems for its hardware line.)

Google already dominates the worldwide market of smartphone operating systems, and Android’s audience is sure to grow as smartphone penetration increases in emerging markets and as late adopters move to smartphones in more mature regions. And initiatives like Google Glass demonstrate that the company is eager to continue innovating. But the online search giant may have to start making some bold moves within its existing ecosystem to avoid becoming the low-rent district of its own mobile platform.