During a recent migration to an MS-driven collaboration environment, we faced the same language dilemma. Longtime Perl programmers, we were (and remain) appalled by the thought of having to use vbscript to automate various system-oriented tasks. In terms of power and flexibility, there really can be no comparison between the two (ih our humble opinions, of course). We found Perl (specifically ActiveState's ActivePerl) to be quite adept for the job, particularly the Win32/Directory Services features, and have used it extensively over the past few months.
We did however find that VBScript was better able to perform certain very specific tasks, particularly those specific to managing certain aspects of Active Directory.
My advice if you require Windows-based automation? Learn both. Even better, learn JScript and Perl. It isn't about the language; it's about getting the job done. Knowing both will help you do that.