I have an apex controller that I'm using to run a SOQL query for some data. Initially, I just had the method return the actual Object, but as I'm making reference to many different parts of data, I've created a new Custom Object (inside the controller) to serve as a "ViewModel" so I can initialize field values and navigate the object more directly in the consuming .js code.

APEX Controller Code:

public with sharing class FundsRequestCostsController {
    @AuraEnabled
    public static RequestTotals getCosts(Id id) {
        if (id == null) { throw new NullValueNotAllowedException(); }

        FundsRequest__c request =
                [SELECT
                    TotalCost__c,
                    ...
                    Campaign__r.NumberOfOpportunities,
                    ...
                FROM
                        FundsRequest__c
                WHERE Id = :id];
        RequestTotals totals = new RequestTotals();

        totals.TotalCost = (request.TotalCost__c == null) ? 0 : request.TotalCost__c;
        ...
        return totals;
    }

    public class RequestTotals {
        public Integer NumberOfOpportunities;
        public Decimal TotalCost;
        ...
    }

    public class NullValueNotAllowedException extends Exception {}
}

Now, when try to access the response object in the .js controller a.getReturnValue() returns an empty object.

Before I made the change to introduce the custom RequestTotals object, it worked fine (having the .getCosts() method return a FundRequest__c object)

I've checked a.getError() and it contains an empty Array.