I can't really comment on past things SE has done, as despite my join date I really only started playing FFXIV in earnest after the ShB announcement and was only getting to HW content by the time it was released.

As it is now, FFXIV's shop seems like the least predatory, clearest with their pricing, and least damaging to its in game economy of all the mmos and many other online games I'm aware of. IMO, this is the ideal way to do a shop, and I generally don't even notice its existence while playing.