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1. Difficult set ups on a small scale. Microsoft provides easy to use GUIs, a novice can set up Active Directory in an afternoon. Have you ever set up a kerberos+ldap+dns system before? It can be quite intimidating if you've never done it before. On a large scale the tides usually turn the opposite direction however...
2. Lame office applications. OpenOffice sucks bad. Almost anyone who uses office can find something that they need to do, that they can't with OpenOffice. The biggest one for me displaying formulas of trendlines. If I make a trendline, I probably want to know what the formula is! This bug has been open for 5 years... literally! The UI is rather ugly and difficult to navigate, and printing is just a half notch above unreadable. Email is also in a sad state. Neither Kontact nor Evolution support groupware of any kind well. Integration is poor, and crashes are common. Most applications have serious usability issues, or lack important features.
4. Lack of specialized applications. Almost all businesses and individuals have atleast one custom or out of the normal application. Usually these special purpose applications don't have a direct equivalent.
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