Looking back I have asked this question since I realized that our Oceanic survivors were not alone..
Tom Friendly: Here we go. Being all sarcastic and leadery, taking Walt...this guy MUST be pretty powerful..NOT! Hes just another lackey.
Desmond: when we first saw him I was SURE that this guy was controlling this Island, pulling strings, pushing buttons...WRONG! He was just pushing ONE button.... and didnt really even know why.
Ben Linus: HERE WE GO, now this is the leader!!!! He has it all figured out right? He is running the show RIGHT!...nope...he answers the the wizard of oz. Just another guy, following another guy, albeit doing an amazing job. Not the head honcho.
Richard Alpert: this guy is EVERYWHERE, he doesnt age! He knows it all, hes seen it all. The secret leader of our island, hes been watching locke since he was a boy because hes the leader, right! NO. If Ben Linus is the dark, he is the light, but not really in charge.
Jacob: Oh thank God, we finally have a leader! Mysteriously undead, time travel, magic touch, funky foot dweller, YES---nope, dead, and ghosty. A silly bumbling mamas boy. Cool lists, cool light house. Oops! his undead brother beat him at his own game. Powerful YES, awesome listmaker, YES YES, loophole proof, not so much.
Adam: OKAY this guy, all dressed in black has got it all figured out. Hes gonna get off that island and kill everyone, hes smokey and everyone who sees him swears he looks familiar. No one can be more powerful than he. Except his mother, who totally manipulated him and clearly hes not over his crazy mother, and still on the island.
Mother: She came out of nowhere. The woman with all the magic, before there was a Jacob. The master manipulator before there was a ben linus. Maybe even smokey before there was a MIB. But shes dead.
So my thought is this. Just when you think you know who's in charge, theres is always some random, awesomely qualified superhuman, whos just Not It. These writers have taken us on a ride where you think its over, solved DONE and then they drop a house on our heads. So instead of complaining about CGI or temple sets, or whatever it is. I am going to sit back and wait, who knows what will happen, I never do.