The way I see it, the strategy of this deck is to use board wipes to eliminate your opponent's threats, and eventually play
Progenitus to win the game.
Now even though
Progenitus has protection from everything, he is still vulnerable. Protection from everything means that he cannot be damaged, enchanted, blocked, or targeted by anything. But board wipes don't target, so they will affect him as well. This is important to keep in mind.
Now, for ways to make the deck better, there is a lot that can be done. First, we can fix the land base. 51 lands is too many (40 seems like a good number for this deck). Replace some of those lands with mana ramp.
Commander's Sphere,
Darksteel Ingot,
Expedition Map, Felwar Stone,
Gilded lotus, and
Lotus Blossom. The rest of the lands need to be able to tap for any color of mana.
Mirrodin's Core,
Mana Confluence,
Gemstone Mine, all make great choices.
There are also some cards that I'm having trouble understanding why they are in the deck (
Proteus staff,
Academy Ruins,
Leyline of Anticipation, Boseiju, and
Firemind's Foresight, to name a few). Try to focus the strategy of this deck, and ask yourself why these cards should, or should not, be in the deck.