Ipstenu, I know those two methods. I'm running a single network. I've got about 150 themes, and I just don't like having to check or uncheck access to that many themes, for every single site. Some users get access to one theme, some get access to all 150. So a full network activation doesn't work, and doing it site by site is incredibly tedious.
Andrea, I know themes are based on sites and not users. The multisite plugin manager works just like I want - it allows me to activate a large number of themes for all new sites, but it doesn't force me to do a network activate, which means I can deactivate the ones I don't want a site to have access to. That's not the ideal solution at this point, but it's a ton easier having to activate on an individual basis.
And maybe to reword what I said before, users will basically use two types of sites - one that has access to just one theme, and one that has access to all the themes. So I'm not saying it's a user based thing, so much it's a choice users make on which type of site they want.
(And to clarify even greater if you're trying to figure out what I'm doing, I run all of my WP sites on one instance. Sometimes I build a custom theme or supply a theme on an individual basis. Sometimes the person wants to do the choosing for themselves and they sift through all the themes and pick one.)