Made some substantial changes now.
Chief among them and what started it:
The removal of Child of Alara.
I like a lot of things about that card (the 5 color mana cost, it having more than 5 power, the trample, flavor/variety, the epic turn-around that happens when an opponent kills it via Ulamog or Heat Ray, how it's a perfect card to take with traitorous instincts...), but I think it's better for it to go. The speed he can get out and the 6 toughness he has makes him a difficult problem, and the Eldrazi player often has great difficulty coming back after losing his Awakening Zone or Dreamstone Hedron in addition to the spawn and what-not. Extra kicker for removal being that this wants to count as a "titan" card, and I only wanted 3 titans per deck.

So what do I put in his place? Well, there's no excellent answer. I settled on a 2nd Mosstodon. Trample, 5+ power ability, ideal for stealing, and lower toughness.

With me breaking the singleton-creature theme, I did it again. Krosan Tusker, which is a little off-flavor since Krosa isn't in Alara or Zendikar, get's replaced for a second Valley Rannet. Benefits here include: flavor, lower toughness, and a slight reduction in card advantage. And maybe making a green-source-less hand keep-able.

Since I took out a WUBRG cost card, Kaleidostone became a little less useful. So it's being replaced by a certainly useful artifact: Etherwrought Page. It's a slow card that does good things, and takes blue and black.

And to help counter the reduction in mana-sourcing that 2 of these changes make, I get to make one more: goodbye beloved Death Rattle.
Out you go for Fiery Fall. It still kills problem cards, but can't be used to take out the eldrazi solo.

So overall, Progenitus' deck's toughness went down, removal became more targeted, and choices went up.

Summary:
Child of Alara -> Mosstodon
Krosan Tusker -> Valley Rannet
Kaleidostone -> Etherwrought Page
Death Rattle -> Fiery Fall