I am doing this quest and I am at the mainframe. I've done the quest before but I was wondering choosing where to put the power, do it make any difference where I assign it other than reputation gain??

Only evil thing you can do is arm archemedes I and gain infamy, and make sure no one like Boone or Arcade are with you, they get PISSED!

I did the full region (not the emergency one)

Sorry didn't mean to post this in this forum.

Depends on your own character, really. Who do you want to side with? What will your conscience allow? What do you, as the character (not the player) want to see done?

Very, very few of the quests in any Fallout game can or are even meant to be minmaxed. Get in your character's head. Put yourself in that situation. Who are you? What do you want? Do you have anything worth dying for? Do you have anything worth living for?

I think all that changes (apart from Archimedes) are some quotes by random people, like NCR troopers that say they want to shoot out the lights of the Lucky 38 if you put the power there.