this is only an issue for a very small % of people who root, I highly doubt it's more than 2 or 3% of people. even on this forum of hardcore users most people don't root, and the general population doesnt even know what the word means
and really, I see what Motorola is coming from. Motorola, HTC, Samsung, all these companies are desperately trying to avoid the fate of desktop PC manufacturers in 90's. They all used Windows, the only differentiator became hardware which brought about a price war which benefited none of them. they all ended up making similar grey boxes. Microsoft made out fine b/c the profits were in Windows.
in a similar way, if Motorola, HTC et all just end up making vanilla Android phones where the only difference is hardware, there won't be much money for them to make. the hardware won't end up being THAT much different from one another, they will be forced to compete on price, and that is a death spiral for them. their solution has been to come up with custom Android UI's (Sense, Motoblur, etc) which differentiate them from each other...but as Android improves I doubt this will really work. Motorola has no history of great software development, neither does Samsung, and even the cool parts of Sense will soon be made redundant by Froyo and Gingerbread
but this is what they get for years of stagnation and letting Apple crush them with the iphone. Google made Android, Motorola made shitty software, and so Google will win. by this time in 18 -24 months or so, my guess is custom UI's are gone.