Migrating to Asp.Net Identity 2.0: new columns not being created in AspNetUsers table

I was having the same problem. I used this manual migration and I haven't run into any additional issues yet.

public override void Up()
{
    RenameColumn(table: "dbo.AspNetUserClaims", name: "User_Id", newName: "UserId");
    RenameIndex(table: "dbo.AspNetUserClaims", name: "IX_User_Id", newName: "IX_UserId");
    DropPrimaryKey("dbo.AspNetUserLogins");
    AddColumn("dbo.AspNetUsers", "Email", c => c.String(maxLength: 256));
    AddColumn("dbo.AspNetUsers", "EmailConfirmed", c => c.Boolean(nullable: false));
    AddColumn("dbo.AspNetUsers", "PhoneNumber", c => c.String()); 
    AddColumn("dbo.AspNetUsers", "PhoneNumberConfirmed", c => c.Boolean(nullable: false));
    AddColumn("dbo.AspNetUsers", "TwoFactorEnabled", c => c.Boolean(nullable: false));
    AddColumn("dbo.AspNetUsers", "LockoutEndDateUtc", c => c.DateTime());
    AddColumn("dbo.AspNetUsers", "LockoutEnabled", c => c.Boolean(nullable: false));
    AddColumn("dbo.AspNetUsers", "AccessFailedCount", c => c.Int(nullable: false));
    AlterColumn("dbo.AspNetUsers", "UserName", c => c.String(nullable: false, maxLength: 256));
    AlterColumn("dbo.AspNetUsers", "FirstName", c => c.String(nullable: false));
    AlterColumn("dbo.AspNetUsers", "LastName", c => c.String(nullable: false));
    AddColumn("dbo.AspNetUsers", "CreatedDateTime", c => c.DateTime(nullable: false));
    AlterColumn("dbo.AspNetRoles", "Name", c => c.String(nullable: false, maxLength: 256));
    AddPrimaryKey("dbo.AspNetUserLogins", new[] { "LoginProvider", "ProviderKey", "UserId" });
    CreateIndex("dbo.AspNetUsers", "UserName", unique: true, name: "UserNameIndex");
    CreateIndex("dbo.AspNetRoles", "Name", unique: true, name: "RoleNameIndex");
    DropColumn("dbo.AspNetUsers", "Discriminator");
} 

Taken from: http://adamstephensen.com/2014/05/02/upgrading-from-asp-net-identity-1-0-to-2-0/

The reason is you've upgraded to Microsoft.AspNet.Identity.EntityFramework 2.0.0.0 and that changes the user context.

To fix either generate a new db (set a new connection string mdf file) or change the sql table.

I had the same problem. Based on what Dan Gershony said, I simply uninstalled the Microsoft.AspNet.Identity.EntityFramework 2.0.0.0 and install an older version like Microsoft.AspNet.Identity.EntityFramework -Version 1.0.0. This solved my problem.