It often depends on a number of things. Sometimes it's hardware related. Other times it's software related. But my guess is that most of the time, many developers don't take the time to test them out on some devices, or they don't have access to some devices for testing. So rather than toss it out there for users to test and risk backlash over it not working, they just mark it as incompatible.
Madden 2012 is an interesting case though. A trial version came pre-installed on my MAXX. I uninstalled it, knowing I had it purchased and the trial version makes you purchase it again through the app. But, as you said, when you go to download it from Play (that still seems weird to say), it says that the game isn't compatible, even though it is clearly compatible because of the demo on the phone. In this case, the developer and Verizon want you to pay a higher price for the game through the demo, so they blocked the device from being able to purchase/download from Play. Very underhanded in my opinion.
