Eventually, when EX aren't around, people will have to choose between running GX Stages or GX Basics. The latter, so far, has had EX-level HP, so perhaps eventually their ease of use won't be as tempting if the Stages can out-perform them. (But like I said, Tapu Lele might be indicating that strong, easy-to-use Basic URs will be around for a long time.)
I am pretty sure you hit the nail on the head here. I am also afraid that Tapu Lele is going to become a 1 of, 2 of, or 3 of in every single deck just as soon as Shaymin EX rotates. Add on the extra hit points and an attack you actually want to use and that card looks broken to me. Maybe not "end of the world" broken, but costs 60 dollars a pop to procure and is absolutely essential broken. Seriously. Jirachi EX and Lugia EX should not have gotten together and produced an heir.
I think this will be the future of GX cards btw and I am worried about the power creep. While a normal "requires 2 turns to stage up" approach to these powerful S2 GXs wouldn't be so bad, I have come around to Otaku's way of thinking regarding the availability and use of stage acceleration cards. I think they made more sense in an era where you needed "anything" to give someone running a stage deck a shot at beating a heavy basic / EX deck. I think in the SM era, these will be abused and will ultimately be very bad for the game.