Do people use S/MIME with the standard (web-based) trust stores? If you're using it with a small group of people you're in communication with, you can always generate your own CA pretty easily with the openssl command.
(Except for the part about the openssl command, this is what Exchange does: everyone joined to an Active Directory domain gets config from the AD servers, so AD generates its own CA for S/MIME certs and tells its users about it.)
I am not a fan of Microsoft in any way and, fortunately, rarely have to touch a Windows box anymore. In a previous life, however, I was responsible for integrating UNIX/Linux systems in a Windows-based environment (i.e., a large organization with thousands of users).
Microsoft's CA services (in Windows) is actually an awesome product. You can create your own root CAs and intermediates and use the included templates or build your own to (automatically) issue certificates for anything and everything that needs to communicate (users, web servers, file servers (including encryption for data at rest), e-mail, etc.).
The CA services are one of the few things I will happily concede that Microsoft did "right" (along with Active Directory and SQL Server).
(Except for the part about the openssl command, this is what Exchange does: everyone joined to an Active Directory domain gets config from the AD servers, so AD generates its own CA for S/MIME certs and tells its users about it.)