Given the highly customizable nature of Linux, configuration files are probably the most efficient method of telling a program what you want. Given a man-page with well-written documentation and some commenting in the config file, making the configuration file is fairly easy.
Unfortunately, the average human being is afraid of the keyboard, or doesn't speak geek-ese, which is what most configuration files are written in. While it is easy for us to understand the syntax of a configuration file, most people would probably have a bit more trouble.
The thing that bothers me is that Ubuntu claims to be "Linux for human beings", yet I still find myself having to edit configuration files, either because there is no graphical version (as with GRUB) or the graphical version is too limited or complicated (as with xorg.conf). Configuration files are not human-friendly. Make a typo and your system could be screwed. Or if your memory is bad like mine and you put the wrong partition number in your grub config file for your Windows partition after the kernel updates wipe out your customized GRUB file. These are things that a simple graphical application could do. Gparted automatically detects the types of the partitions, why can't there be a nice little boot settings manager installed by default?
I believe that configuration files are also something that deters the semi-technical users from Ubuntu. These are people who understand computers, learn the Linux system and try to fix things for themselves. Unfortunately, they don't really know what they're doing and don't really want to spend a lot of time to get things to work. They think, "editing a config file, that's not so bad", mess it up, and then have a whole lot more problems than they had originally. They then go "Windows works, Linux doesn't" and switch back to Windows with a now soiled reputation of Linux in their mind for the next ten years. They then go and tell all their semi-technical friends about their experience, and further soil Linux's reputation - given the usability of the average Linux distribution, this reputation is not entirely undeserved.
Ubuntu should definitely iron out these usability situations, and quick. Since Ubuntu is hitting the mainstream with Dell and Asus selling Ubuntu PCs, it would not be good for Ubuntu to get a reputation as unusable in the mass market.