It's not the linux desktop itself that is rough around the edges, so much as the applications being developed for it. Commercial developers who provide a linux version often do so as an afterthought, and it shows. Open-source developers tend to produce apps that work, but lack the fit and finish of the commercial product, especially in terms of interface design.
As for "keeping your system clean", the very nature of Linux makes that sort of operation much less necessary. System files are segregated from user files, and it's generally only the user filespace that gets cluttered, not the system. So the only reason to worry about it is disk usage, unlike Windows where the filesystem and registry can get completely borked over time due to user additions.