I don't consider myself an expert on this stuff, so do treat my advice with a large dose of salt...
Consider taking a more pragmatic approach. Do you really need repositories, or is it just "following best practice"? By going down the repository road, you create complexity and indirection in your code. It takes time to set up and learn how to do it "properly".
Ask yourself what benefit you will get out of using repositories. You should have a clear, practical reason -- not just "oh well, maybe one day I might want to swap out my Eloquent models for something else."
Repositories do have uses even in smaller applications where you depend on Eloquent. In particular, they can be useful places for storing the kind of query logic that you mentioned. But consider just stuffing it all in the model for now. Okay, so you have a few extra methods on your User model. Big deal.
Avoid turning your repositories into wrappers for Eloquent. You can either have the convenience of Eloquent, or the abstraction of an "implementation neutral" data access layer -- but you cannot have both. Many developers have wasted a great deal of effort trying to square this circle. If you use Eloquent, you must accept that your code depends on it.
Even if you use repositories, don't make one for every model "for consistency". Add them for models where they are actually useful.
There is nothing wrong with having to modify your controllers. This not a compelling reason for increasing abstraction. However, what if you find yourself wanting to use the same logic in two different places -- say in two controllers, or in a controller and an Artisan command? That is a good reason for abstracting the logic into another class, which could be a service class, or a command/job.
Normally a command/job would be dispatched from a controller. The controller says, "I have received valid user credentials for a new account. Now, UserRegisterCommand, kindly do my bidding and carry out the tedious work. I care not for such petty matters." *waves hand imperiously*
I'm not saying that abstraction is "bad". What I'm trying to say is that abstraction has a cost, and much of the time it's just not worth the hassle.
My rule of thumb is that I abstract stuff when I feel "pain", not because someone somewhere said that I shouldn't have application logic in my controllers or query methods on my models. "Code purity" is not the goal. The goal is to avoid making life hard for yourself.