No you're missing it entirely.
To put it in short instead of a wall of text, in an ideal world:
PvP endgame gear = For PVP content only
i.e. Warzones and open world PvP (maybe good enough for planetary dailies but they don't have much of a gear requirement but useless for harder endgame PvE content like flashpoints and operations)
PvE endgame gear = For PvE content only
i.e. Flashpoints and operations (focus on player vs environment content but useless for warzones).
Okay, fair enough.
Whats so bad about the way it is right now?
Edit: From the beginning I understood this was what you wanted.
It was the WHY I was trying to understand. It sounded like you were addressing some sort of "unfairness" which is the point MY posts were trying to speak to.
Edit Edit: I really don't have a horse in this race. I tried PvP for a while, didn't really like it, don't do it anymore. So your wishes could be fulfilled and it wouldn't affect me in the slightest. It just doesn't make sense why you're insisting on this.