Upgrade from 2.x to 3.x: zillion of changes required?

I have started to upgrade a project to 3.x. The upgrade tool was some help but now I’m stuck with tons of minor, but still necessary changes.
Think of a Table “Users” with a belongsTo - relation to Groups. Now in the UsersController In 3.x I read one user as
$user = $this->User->get($id, [‘contain’ => ‘Groups’]);
quite similar to what I did in 2.x
In 2.x I had to access (database) fields like
$user[‘User’][‘id’] or $user[‘Group’][‘id’]
That doesn’t work in 3.x, I have to change this to
$user->id or $user->group->id
And that in a lot of places. And if I miss one the code will not work.
Am I doing something wrong? Is there an easier way to do those changes?
I asked Google but all blog entries about upgrading told of “some work” in the ORM but none of the zillion changes you have to do in Views / Templates or in the Controller or elsewhere …