I don't think it is so much that it gets in the way of root users, but it IS getting in the way of normal users. Phones that have Blur on them still can not get the update to 2.1 because Blur has to be updated by Moto to run on it (from the reviews what is running on the X will not cause this problem so that is a good thing). The same thing is happening with some of the older phones that run Sense (although it isn't as bad from what I hear)...
For me as someone who is rooted, it is all about my personal preference... I just prefer the look of stock Android and don't want all that UI stuff pre-installed. If I do there is always a theme or a ROM that I can get to make pretty or get the widgets