Skipping Energy Controllers
From M2K2: Metroid Prime 2 Wiki
If you defeat the boss of a dark temple, and go to the room where the dark energy controller is, but do not actually collect the energy, the yellow "you cannot leave this area" things do not pop up on the exits. Meaning, if you don't get the energy, you can skip returning it entirely.
You need to visit the energy controller room to make the game reload the temple and allow you to leave. Just don't walk far enough into the room to start the "getting the energy" cutscene.
