The big problem for Motorola is one we've heard before: they're not happy with the fact that Android is becoming the Windows of the smartphone world. The company can't differentiate enough, making it harder to compete. Making Android skins is one thing, but HTC, LG, SonyEricsson, and Samsung are doing the exact same thing. It's crowded in there.
It's not just the inability to differentiate; other issues that supposedly underpin Motorola's the desire to develop its own smartphone operating system are the recent extortion attempts against Android vendors, Android's fragmentation issues, and Google's support for its partners - which I'm assuming means 'or lack thereof'. It seems a little bit odd to mention fragmentation as a reason to develop your own operating system, but okay, we'll roll with it.
Motorola has also been on a hiring spree, snapping up several former Apple and Adobe employees. "Over the past nine months, Motorola has been hiring engineering talent that would well-suited to create a new mobile operating system," InformationWeek claims, "Its team appears to include a significant number of ex-Apple and Adobe personnel, including Gilles Drieu, VP of software engineering at Motorola Mobility, Benoit Marchant, director of engineering at Motorola Mobility, and Sean Kranzberg, also a director of engineering at Motorola Mobility."
Motorola, for its part, declined to comment but did say they are fully committed to Android. Pulling this all together, I'd say it makes a lot more sense for Motorola to simply continue building on top of Android, leveraging the work they've already done on Motoblur. It's fully possible to develop an enticing, differentiated interface on top of Android, without harming application compatibility.