I don't think I understand what the difference is with the "old way" if as you describe it ... there seems to be no difference. You don't have to pay some cert provider under the old or current way.
Perception is everything in those first few moments a user get his hands on your software. But now if I dont pay the entrance fee I potentially get abandoned by said user bc they have been scared off.
Its not an app store yet. Give it 5 or 10 years when we no longer have an open web and all we have are walled gardens.