If you are wanting a five color general, you may want to consider one of the others because Progenitus gets shuffled into your library every time it dies.

Incorrect JIV_IV. Putting a commander in the command zone is a replacement effect that the owner of the card has the option to do when the card would be put into their graveyard/into exile.

903.11. If a commander would be put into its owners graveyard from anywhere, that player may put it into the command zone instead.

The owner of the commander has the choice to do one of the the two replacement effects (shuffle into deck, as written on Progenitus, or to put it in the command zone), and whichever they choose is the effect that happens.

Well, it seems that you would be correct. You have my apology.

On top of that if you noticed there is creatures like Bringer of the Black Dawn and other effects with wich I have no problem on getting something from my lybrary

I would suggest slightly skewing your mana base to be maybe 30% green then play all the good green mana fixing, Cultivate , Kodama's Reach , Explosive Vegetation , Yavimaya Elder and Oracle of Mul Daya . If you don't want to use green ramp I would look into the guild signets from the original ravnica, Rakdos Signet , they're basically rampant growth.

Some cards I'd suggest for no particular reason include Propaganda , Collective Restraint , Recurring Insight , Temple Bell , Hex , Mogg Infestation , Boundless Realms .

Thanks for info about those signets. I completely forgot about them but maby those new cluestones would be better option( Gruul Cluestone etc.) since they mana cost is similar and on top of that they have card draw? Also I have no idea what to remove from this deck...

The signets are by far better because they cost 2.

You might consider dropping Blessings of Nature , Sadistic Sacrament , Rhystic Tutor (bad in multiplayer), Mask of Avacyn , Jolrael's Favor , Blood Reckoning , Archmage Ascension (unless you add Temple Bell and Howling Mine ), Hunger of the Howlpack , Back to Nature , and Erase .

In other words I think your non-creature spells need work. Some go to cards include Relic Crush and Return to Dust , Bant Charm for commanders, Mirari's Wake and Mana Reflection , Aura Shards , Supply/Demand is a cool card, Rite of Replication , Mogg Infestation , Phyrexian Arena .

I'm not sure but I hope this helps.

I have a Progenitus edh deck myself and would like to help a fellow hydra lover. Being that said first you need to get rid of 25 cards even before starting to build your deck for real. First question is how do you plan to win? Since you can practically put any card that is available to commander format this is one of key questions you need to answer. If you plan to use your commander than I highly suggest these four cards Rafiq of the Many , Finest Hour , Maelstrom Wanderer and Urabrask the Hidden first two cards lets you finish a game in one turn with your commander. Last two cards lets you attack with your commander as soon as you cast so it won't get swept by mass removals.

If you are planning to win by overwhelming your opponent with your creatures last two are still good choices since maelstrom cascade twice for 7 cmc or lower and urabrask not only give you haste but also annoys your opponents.

I also suggest puting more tutors to fish out keycards for your win conditions or straight out your mana base.

Since you have Prismatic Omen you can try Koth of the Hammer for almost doubled mana or all lads having pimp damage thanks to his emblem.

I strongly suggest getting a Sorin Markov his second ability leaves any one opponent with 10 hit point which concidently how much a bare Progenitus hit :P

Depending on your decks style forming (creature base, control base, planeswalker base, commander base etc) there will be more suggestions.

@greenstalker Thanks for suggestion. Yea i'm planning on using it, but not that much. My wincon is simply make huge hydras and swing at everyone with everything including Progenitus . I was thinking about adding haste cards to my deck, but later decided that it's not that much needed for me anyway :) although I must say that Urabrask the Hidden is quite tempting :) most of the time I'm playing multiplayer so there won't be much use from koth and sorin. And cascade for my deck can be quite dreadful wwth x mana cost hydras. Completely forgot to add Academy Rector to my deck :D

Looking at the deck, you could use for a few more board wipes in order to last longer and get more mana to cast things. Wrath of God and Supreme Verdict are both very good for this. Supreme Verdict more so because it can't be countered.

Smith_and_Tonic I can agree with that but atm my bigger problem is extra 21 card that I must remove from this deck

Elvish Piper and Quicksilver amulet

Both of them have same problem... My deck is based around hydras which are x cast...

Well if you get 4 mana you get progenitus and whatever else you want out on turn 5 It doesnt particularly matter if it doesnt cost X

from hand. progenitus is not in my hand

Add in a Demonic Tutor then

It's already in the deck :) in total I have 3 tutors in my deck

Well Piper will work then

You could also put in an increasing abition

I have putted in Diabolic Revelation instead of ambition. ambition gives you 3 cards for 13 mana. with revelation for 13 mana you can get all hand

Hmm,what about Rosheen Meanderer?

Originally he was in the deck, but I had to remove him due to too many cards.

+1 for having Rock Hydra

Doubleo it's my favorite :) a lot of people offered to remove it from deck for other cards but I allways refused :)

you forgot Polukranos, World Eater