Given a choice, most enthusiasts would prefer a stock build of Android on their smartphone, and the preference towards an unmolested UI is part of the reason people root. But not everyone has the know-how or courage to root, even though smartphones sporting custom UIs far outnumber ones with a stock build. The reason, according to Motorola Mobility CEO Sanjay Jha, is because it's tough to make money on stock devices.
"Verizon and AT&T don't want seven stock ICS (Ice Cream Sandwich) devices on their shelves," Jha told The Verge in an interview during CES 2012.
He pointed out that Motorola and other carriers have to make money and there's just no way to profit on a device that hasn't been tampered with.
"The vast majority of the changes we make to the OS are to meet the requirements that carriers have," Jha said.
Whether you want to call it "differentiation" like Google's Eric Schmidt does, or view it as fragmentation, it really doesn't matter. As long as carriers think there's no way to flip a buck or two on a stock build of Android, such devices will continue to be the exception to the rule.