Skuzzy you're looking at this from a specialist angle Regular users can never handle things like user rights management in linux - way too complicated for every day regular use. I know this from experience after trying to introduce linux to non computer savvy people.
Either you preconfigure the linux box so that the user has everything (and I mean everything) ready and working or you're stuck with endless fix'em up calls.
The second problem is lack of software. Most commercial software is available on windows only, heck some are only available in DOS still.
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That is what IT is supposed to be for. Bunch of lazy chumps these days. I took a bunch of engineers from Apple to UNIX in less than a year. Yes, I configured the boxes from top to bottom as the IT guys had no clue what to do . Engineers are the most anal retentive people you will ever meet.
Software will simply depend on what needs to be done and how you want to do it.