To understand how you should structure response data from the Apex controller, let's take an example of Apex code that is needed to display a list of accounts for a Lightning Component:

public class AccountController{

    @AuraEnabled

    public Static List<AccountWrapper> queryAllAccounts(){
        List<AccountWrapper> accountWrapperList = New List<AccountWrapper>();
        List<Account> myAccounts = [Select id, Name, BillingState.
                                           (Select id
                                              From Contacts)
                                      From Account];
        if(!myAccounts.isEmpty()){
            for(Account currentAccount : myAccounts){
                accountWrapperList.add(new AccountWrapper (..) );
            }
        }

        return accountWrapperList;
    }

}

This is the message/wrapper class code:

public class AccountWrapper{
        @AuraEnabled

        Account currentAccount;

        @AuraEnabled
        Integer noOfContacts;

        @AuraEnabled
        Boolean isPartnerAccount;

        @AuraEnabled
        //Few more variables

        public AccountWrapper(Account currentAccount, Integer noOfContacts, Boolean isPartnerAccount,..){
        
            this.currentAccount = currentAccount;
          ....
        }
    }

Note that in this scenario the service is returning responses as a custom Apex type. It has been observed that using a JSON string as the response type improves the performance, compared to the return type of Apex that is custom-defined. The platform under the hood suffers from some performance issues, and this is more noticeable with large datasets.

Instead, we can return as the JSON, using the following code snippet:

public class AccountQueryController{

    @AuraEnabled

    public static String queryAllAccounts(){

        List<AccountWrapper> accountWrapperList = New List<AccountWrapper>();

        List<Account> myAccounts = [Select id, Name, BillingState.
                                           (Select id
                                              From Contacts)
                                      From Account];

        return JSON.serialize(myAccounts);

        }

You can then parse the string response into a valid JavaScript object, using JSON.parse() on the JavaScript. It has been observed that the performance is significantly improved via this method.