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A big disadvantage is disk space. Creating many filesystems can get expensive, but there are some ways to combat this. If users on a virtual server do not need X-Windows, don't copy it over (and files supporting it). If users do not need Emacs, don't copy it over, and so on. For each virtual server, you can pick and choose what should reside on it. Just as long as the important base system (in addition to what services each virtual server needs) exists it should be fine.
You can hard link binaries from the main server to your virtual servers, that need to be used. When I create virtual servers, they usually take up about 10-15 MB.
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