Andrew Nacin's analysis rings true to me. But In the future with any changes that alter the advertised behavior of a standard WordPress installation, you could get the best of both words, so to speak, by making a point of preserving existing behavior *for updated installations*. I don't think it would be too bad to default to whatever you think is best for new installations, because those users will be able to strongly correlate installing your plugin with whatever the change in behavior is.
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