Because that was not their goal before, they were OK with the level of freedom their users had with stock Android. With the future restrictions Google will apply to Android they are probably looking to ship their new devices with Graphene to prevent that.
I used Motorola's products with Android for years and they one of the few in the market to still deliver something close to stock Android with only a couple of apps added for specific features (gestures to turn off flash lantern, etc) so I don't where you got this malware thing going on with them. Unless you count everything Google as malware, in that case yes.
Now I got a Samsung and it's one of my worst experiences ever using their "One UI" and it is really riddled with crap because Samsung for some reason thinks they need to add their own versions of every app included in stock Android.
Well yeah everything is a choice when trust is the matter, but there is a difference between choosing a community project that can be audited by different transparent parties and choosing a private company on their own servers (even on source available projects)
Not explicit enough