Page Types and their settings are per project.

Do you have different editors for each site? If so you can say that editors for SITE A are the only ones to have access to create pages of type A while editors for SITE B are the only ones for pages of type B.

Another solution would be to have all your Page Type specifications as abstract classes, create implementations per site and have limitations using the Include attribute. Can be a bit messy to manage though.

A third spontaneous solution is to build the structure per site using T4 Templates.

You can use the [Access] attribute to lock the availability of page types down to certain groups/users. This affects the access level which can be seen in admin mode > content type > [your page type] > settings > access level.

http://world.episerver.com/Documentation/Items/Developers-Guide/EPiServer-CMS/75/Content/Attributes/#Access

Also if you didn't want to manually add people into groups you could create a virtual role and control membership of the group in code.