I'm not sure how this will be handled in the final release of ASP.NET 5, but in the case of ASP.NET 5 RC1 we have the following:
Firstly, you should go with Identity 3.0, as there is no way to use Identity 2.x in MVC 6 as far as I know.
Secondly, to make Identity 3.0 work with EF6, you need to implementation your own "EF6-friendly" versions of all classes under Microsoft.AspNet.Identity.EntityFramework namespace (the code is available here- https://github.com/aspnet/Identity/tree/3.0.0-rc1/src/Microsoft.AspNet.Identity.EntityFramework), as original classes are meant to work with EF7 only:
- IdentityDbContext
- RoleStore
- UserStore
- IdentityRole
- IdentityRoleClaim
- IdentityUser
- IdentityUserClaim
- IdentityUserLogin
- IdentityUserRole
Your implementations should utilize EF6 instead of EF7. The process is pretty straightforward, but if you want to save time, I have shared my implementation here:
https://github.com/EntrypointSoft/AspNet.Identity.EntityFramework6