It’s hard for Andy Rubin and his Android creation to catch a fair break.  Partnering with just about every carrier and smartphone manufacturer, Android has come from nowhere to be the dominant OS in the smartphone industry in under three years.  Windows Mobile was scrapped, Symbian was cut and now Blackberry and Windows Phone 7 are in a fight to gain some pittance of market share against the surging Android.

Android’s growth has even made Apple’s iPhone, which continues to grow in numbers, flat in market share.

When I go into a Best Buy (BBY) nowadays, I see about 40 Android devices next to a few feature phones, an odd BlackBerry or Windows Phone 7 and a few iPhones.  Walk into a Radio Shack or most U.S. carrier showrooms and you’ll see the same thing.

So you’d think the news would constantly be on what Android is doing right?

That’s hardly the case.

I spend most of my day wading through reports of how Android devices are too cheap or that the user interface is ugly and either too much or not enough like the iPhone’s.  The quality of the apps aren’t up to snuff or the screens are too big or small, the battery life is horrible and the phones are too thick.  On and on.

This, for the mobile OS that is destroying everything else out there.

The two biggest complaints I hear are that Android devices don’t get updated quickly enough (True!) and that Android devices are fragmented — which is a symptom of the first problem.  Manufacturers and carriers aren’t motivated to update their handsets to the latest version of their OS because they want to sell new handsets, not keep their customers on old ones.

Add to that, carriers and manufacturers add complicated and often crippling overlays to Android, which make it that much more complex to upgrade.  That’s why Google’s Nexus products, those sold free of carrier or manufacturer excesses, are so important. They get updated swiftly and give you the real Google experience.

But the Nexus initiative wasn’t enough.

According to Businessweek, Google has spent the last few months trying to fix the latter two problems.  By enforcing its long held “anti-fragmentation” measures, it is telling carriers and manufacturers that they can’t get too crazy with their modifications.  I imagine that the companies that upgrade their devices after releasing them are being treated better than those that don’t.

But that doesn’t sit well with many who decry Android’s ‘Open’-ness as a free ticket.  Google, which seemed to have some foresight when building out the Android developer license, gave itself some controls so that the open source platform didn’t get too out of hand.

There was similar outrage when Google announced that it wouldn’t publish the source code to Honeycomb until it had cleaned up the code.

Android 3.0, Honeycomb, was designed from the ground up for devices with larger screen sizes and improves on Android favorites such as widgets, multi-tasking, browsing, notifications and customization. While we’re excited to offer these new features to Android tablets, we have more work to do before we can deliver them to other device types including phones. Until then, we’ve decided not to release Honeycomb to open source. We’re committed to providing Android as an open platform across many device types and will publish the source as soon as it’s ready.

Other options are opening for manufacturers and carriers that don’t want to play Google’s game but still want access to the Android code.  Amazon now has a fully functional App store which gives device makers a way to enjoy apps without Google’s default market — which only comes on approved devices.

Indeed, CellularSouth just released the first Android device with Amazon’s Appstore in the default install.

Facebook and Microsoft (MSFT) have also been edged out by Google.

Google’s Rubin says that such clauses have always been part of the Android license, but people interviewed for this story say that Google has recently tightened its policies. Facebook, for example, has been working to fashion its own variant of Android for smartphones. Executives at the social network are unhappy that Google gets to review Facebook’s tweaks to Android, say two people who weren’t comfortable being named talking about the business. Google has also tried to hold up the release of Verizon  Android devices that make use of Microsoft’s rival Bing search engine, according to two people (VZ) familiar with the discussions.

While it seems intuitive that Google would want to limit the benefit that both of these competitors could derive from Android, by using clauses in the Android developer license, it doesn’t sit well with people who simplify Android as “open.”

Both of those companies are likely heading to the Justice Department over these issues.

It’s these types of actions that have prompted the gripes to the Justice Dept., says a person with knowledge of the matter. Google spokeswoman Shari Yoder Doherty declined to comment on Google and its partners or any complaints to the government.

For what it is worth, almost two-thirds of Android devices that have checked into the Android Market in the past two weeks were running Android 2.2, a relatively recent version of Android.  The second most popular flavor is Android 2.1 which, combined with 2.2, makes up over 90% of all Android devices.

EETimes extends this concern to chipmakers saying that Intel isn’t getting a fair shake.  Interestingly, the exact opposite is true for Android-powered GoogleTV, which is Intel only, at least for the moment.

How will the carriers and manufacturers react?  One option for some is heading over to Microsoft’s Windows Phone 7 or developing their own Smartphone OS.  Motorola (MMI) has been rumored to be doing just that (they had a Linux distribution before Android, which was poorly received) so it isn’t clear if they think they can now do better.  Samsung has its Bada smartphone OS, which it puts on its low end phones, and also sells Windows Phone 7 devices like the Focus.  HTC, ASUS and LG are in a similar situation, building both Android and WP7 devices.

Windows Phone 7 is still an unproven ground for manufacturers, and with the recent Nokia arrangement announced, they have to wonder if there is favoritism there as well.

What do the pundits, who just this week were complaining of Android’s fragmentation, think of the move to clean up the perceived mess?

Android is no longer open and Google starts asserting control. Andy Rubin, Vic Gundotra, Eric Schmidt: shameless, lying hypocrites, all of them.

Poor old Android can’t catch a break.