Now that I'm thinking about it, it makes me wonder if anything was missed on the way to Serenity City...but I don't think anything CAN be missed. You have to do Groment Mines to unlock that Gym, complete that Gym to be able to Surf, and then along Route 412 you go. Provided you didn't use a walk through walls or something, you can't end up in that scenario with the Leader missing from the Power Plant.
However, since Electivire is having level bugs in your copy, you need to replace it with the current copy and try that. Not only will Electivire work, but perhaps the Leader will show up. If I can learn how to remove the flag blocking his appearance (which would require more tools, not something I have time for today), I can set him to appear all the time until spoken to, then he's gone again as before once the Gym is unlocked. However, I'd have to use a copy (or back up the original) because I don't want to do something like that to the main game file I'm working on, which doesn't have this bug.
One more thought. Are you using Save States? Save in-game and then reset the ROM and load it, see if that fixes it.
Edit: Okay I applied the patch over it and loaded it up and what do you know, hes standing there now, now I guess I can go get my electivire too. This is great thanks for your help.