I think the original idea would've been a bolder choice and the storyline perhaps would've made more sense and been more satisfying. Even when they went in another direction, they seemed to have kept most of the previous storyline so the new tacked on ending just didn't feel right, particularly when Salvation remained more of Marcus's story than John's.
I definitely think a cyborg leading the resistance would be pretty ironic, interesting and open up some moments of character development/interaction sorely lacking from Salvation. How would his cell respond to him after the transplant? How would he feel? It would be this big secret that they would have to keep I suppose and could add a lot of internal drama, tension, and suspense.
Where it stands now is that John's relationship with his cell hasn't changed. They respect and revere him just like at the beginning of the film. Its a pretty static relationship. He still has to convince others that he's the best leader to follow I suppose, but I don't think that's as interesting as him having to do so while hiding such a big secret. Making him a cyborg adds an element of doubt, of fear, and perhaps even discovery that might have taken the Terminator franchise in a direction that really added something new to the Terminator franchise and made us see what came before in a different light instead of just playing in Cameron's, Hamilton's, and Arnold's sandbox, which isn't that bad since they constructed an awesome sandbox. It's just not that fresh.