Only User Model is saving with empty Values to database

The reason is most probably the new middleware in Laravel 5.4 called "Request Sanitization Middleware" as explained in https://laravel.com/docs/5.4/releases.

Disable \Illuminate\Foundation\Http\Middleware\ConvertEmptyStringsToNull::class, in app/Http/kernel.php and see what you get.

You can also check in /config/database.php and your mysql connection settings: 'strict' => true, if so, set to false.

A good practice is using the model for user input. In this case, instead of $user = $this->model->create(...) populate you model with $user = new \App\User($input) and update your values from there, f.ex. $user->confirmation_code = md5(uniqid(mt_rand(), true)); and $user->password = bcrypt($user->password);

If fields are nullable, indicate as such in your migration file, f.ex. $table->string('all')->nullable();

If done just run $user->save();

From 5.4 the create() function is not more defined in Illuminate\Database\Eloquent\Model:

Is handled as dinamic method call, that is by calling one of these functions (dependig on if it's called statically or not):

public static function __callStatic($method, $parameters)
// or
public function __call($method, $parameters)

In the Illuminate\Database\Eloquent\Model class.

Now I dont have all your code but, IMHO, I will try to change this line in your BaseModel class:

return parent::query()->create($attributes);

to this:

return $model->create($attributes);

or, even better for me, to this:

return (new static)->newQuery()->create($attributes);

In the documentation it says:

$post = App\Post::find(1);

$comment = $post->comments()->create([
    'message' => 'A new comment.',
]);

So

$user = $this->users()->create([
            'first_name'        => $input['first_name'],
            'last_name'         => $input['last_name'],
            'username'          => $input['username'],
            'email'             => $input['email'],
            'password'          => bcrypt($input['password']),
            'confirmation_code' => md5(uniqid(mt_rand(), true)),
            'confirmed'         => 1,
            'api_user'          => (isset($input['api_user']) ? $input['api_user'] : 0),
            'account_id'        => $input['account_id'],
            'role_id'           => (isset($input['role_id']) ? $input['role_id'] : 0),
            'all'               => (!isset($input['associated-permissions']) || $input['associated-permissions'] == 'all') ? 1 : 0,
            'status'            => (!isset($input['status']) || $input['status'] ? 1 : 0),
            'all_locations'     => $input['all_locations']
        ]);

where users() is your public function but I don't know what is $this in your case but should be the model as in the example from documentation.

Why you're not using resource controllers? Or if you need to populate the db use a seeder I think It will be more easy to manage.

So 2 things i can think off

1st there is no need to use

protected $guarded = [];

and

protected $fillable = [];

Guarded will assume everything is fillable if its not in here and fillable will assume everything is guarded unless in here.

To quote the docs

While $fillable serves as a "white list" of attributes that should be mass assignable, you may also choose to use $guarded. The $guarded property should contain an array of attributes that you do not want to be mass assignable. All other attributes not in the array will be mass assignable. So, $guarded functions like a "black list". Of course, you should use either $fillable or $guarded - not both.

2nd to rule out any of the $this->model stuff try instantiate the class first and save them

use App\Path\To\Model as user;

$user = new user();
$user->first_name    = $input['first_name'];
$user->last_name     = $input['last_name'];
$user->username      = $input['username'];
$user->email         = $input['email'];
$user->password      = bcrypt($input['password']);
$user->confirmation_code = md5(uniqid(mt_rand(); true));
$user->confirmed     = 1;
$user->api_user      = (isset($input['api_user']) ? $input['api_user'] : 0);
$user->account_id    = $input['account_id'];
$user->role_id       = (isset($input['role_id']) ? $input['role_id'] : 0);
$user->all           = (!isset($input['associated-permissions']) || $input['associated-permissions'] == 'all') ? 1 : 0;
$user->status        = (!isset($input['status']) || $input['status'] ? 1 : 0);
$user->all_locations = $input['all_locations'];
$user->save();

Yes, you can't use __construct method in Traits.

Please Refer PHP.net for more details about trait, they said "Using AS on a __construct method (and maybe other magic methods) is really, really bad."

You can use trait like following way.

class User extends BaseModel
{
    use userRelation
}

Trait userRelation
{
       public function getUserName()
       {
             return "Jhon Doe";
       }
}

I have created "userRelation" Trait which contains few useful code to re-use.

Please refer following link for more details - http://php.net/manual/en/language.oop5.traits.php

Please try it and let me know if it won't work. Thanks