Yes. There are quite a considerable amount of limitations in the limited edition. For an example.
The user cannot add additional dialog screens apart from the given by default.
Limitations when defining Custom Actions.
The user only can define banners and main image to setup.
All it can do is extract the given files, folder structures which are defined in the solution.
There is no harm providing a basic output setup using Install Shield Limited Edition.
There are no trial periods, user can continue using limited edition as long as they like. And can switch to professional, premium whenever they like.
The differences between limited and other versions is, that the user can define custom actions, get user inputs to dialogs and add custom dialogs to the setup wizard.
I suggest you to have this extension (https://visualstudiogallery.msdn.microsoft.com/9abe329c-9bba-44a1-be59-0fbf6151054d), which is the same windows installer plug in that allows you to work with as you were working in Visual Studio 2010 deployment project type.
(update on 24-02-2017)
Or if you like a little action, I suggest you to use windows installer XML extension.
Hope this helps.