Here are some ideas for your deck:

-You won't be able to use it as your companion, but Jegantha, the Wellspring will be a helpful ramp card for the deck you're building.

-Bonfire of the Damned can help knock down an opponent's battlefield and feed into Zaxara, the Exemplary.

-Unless you're willing to find a spot for Ramos, Dragon Engine you may be better off replacing Door to Nothingness with Mayael's Aria. In part because of the activating cost, and in part because if the game stalls out Mayael's Aria is more likely to get you a win in a multi-player game.

I hope this helps. Thank you for reading me out. Happy Hunting.

TheoryCrafter, I'll definitely cut Door for Mayael's Aria, and I will consider Bonfire since it looks interesting. The Door is cool, but unfortunately, it's more of a flavor win. I appreciate the suggestion! Are any of the other hydras listed worth considering? If so, what would be good cut options? I am having trouble cutting cards at the moment.

Also, since I have Fist of Suns, Jodah, Archmage Eternal, and a few other relatively similar cards, Jegantha might not make the cut. Another reason is not maximizing Jegantha's mana ability due to the color imbalance and how my deck is mostly green, but I will consider it since it DOES half Progenitus' cost without the tax.

Of the Hydras listed I'd go with Managorger Hydra, Mistcutter Hydra, Savageborn Hydra, Shivan Devastator and Steelbane Hydra. All of these because of the in their casting costs.

However, at this point you may have to choose between doing Hydra tribal or forgetting hydras altogether and put Progenitus in your deck and Jodah, Archmage Eternal in your command zone. Because paying instead of will only result in Hydras without toughness.

While your deck is unbalanced in favor of green, Green is the best color for mana. You can also include in your deck including, but not limited to, Cryptolith Rite and Jiang Yanggu, Wildcrafter.

As for cuts you have a lot of Ramp/Color fixing. You may want to start there. I'd consider start with any card with with a mana value of 5 or higher.

Thanks again TheoryCrafter! I made cuts and changes based on your suggestion. I did my best to keep a balance while adding more cards for Zaxara, the Exemplary and Unbound Flourishing.

Cuts made:

Forgotten Ancient, Jodah, Archmage Eternal, Fist of Suns, Bootleggers' Stash, and swapped a few lands.

Cards added:

Shivan Devastator, Steelbane Hydra, Unbound Flourishing, and Bonfire of the Damned.

I still want to implement Progenitus' commander damage strategy on top of the hydra tribal idea, so I kept many of the exalt cards and mana fix/ramp. Another reason is that the ramp cards assist with values too.

As for Cryptolith Rite and Jiang Yanggu, I will consider them. I might cut Joiner Adept for one of them.

Duneblast works well with one big boss. Spark Double doesn't target so you can have Progenitus twice (or any other creature you want to copy)

Breath of Fury doesn't need that expensive dragon. Either of the Krenko's work fine with half the CMC.

carpecanum, thanks, I appreciate it man! I'll try to include Duneblast or Spark Double somewhere -- I never thought of them. The dragon is included more because I have no commander decks that rely on combat or creature-focused/heavy decks, and I own one so I slapped it in; I doubt the jank interaction with Breath would work. It's also a threat on its own but I'll potentially cut it.