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The filesystem, for instance, is an unbelievable mess in every way shape and form. New users will have no idea what filesystem to use, and once they figure that out they still have to figure out where to put stuff, and how to manage all the crap that they don't care about.
In Linux, you want a place for your documents? It's called your Home folder. It's easily accessible and nicely labelled. You need to know absolutely nothing more about the filesystem hierarchy to use Linux. Since all programs are installed either through Synaptic or via .deb (or .rpm if you're so inclined) files on the internet, configuration files, binaries, images and so on are all intelligently installed in the right place. For a typical user, they don't need to pick what filesystem they want since the installer picks it for you. This is just nitpicking now. If somebody installs XP then they have to decide whether they want FAT or NTFS. It'll automatically choose NTFS for you (an Ubuntu installer will automatically pick ext3). Case closed.
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Next we've got the whole linux system in general. It should really be invisible to the user. The average user doesn't give a crap about what renders the desktop, what manages the network, and so on. They just care that it works. And with Linux, there's a good chance that it doesn't. While I don't like to say it, large parts of Linux just don't work the way they should. I can't connect to any other computer on my network from Linux. I don't know why, and I don't really care, but that's reason enough for me to stay with Windows.
And how does Linux try and tell everyone about the programs it uses? People will find out if they're interested but everyone else will just pick "Firefox Web Browser" or "GIMP Image Editor" for web browsing and image editing. It tells you what they are in the name. People who are actively interested may try and learn more but there's no forcing people to learn to find out about stuff. As for issues like not connecting to a network, that is a problem with licensing (i.e. Samba). Any driver issues are the fault of the companies who make the products because they never made any drivers for Linux. My laptop works absolutely (and I mean absolutely, wireless, bluetooth, graphics, sound, card reader, touchpad) with no flaws. My friend's desktop (custom built) runs with no issues either. Don't be so quick to blame the operating system because it isn't widespread enough just yet.
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just so that they seem different from Windows.
So you're saying every other operating system should copy Windows? NEWS FLASH: Windows isn't the baseline by which every single operating system should conform. Windows might do some things well but not everything is perfect. Different operating systems have different ideals for a perfect desktop (i.e. look at
Symphony) and it's not right to say that every OS should just copy Windows. Besides, if they did then what would the point be in originality?