This control deck primarily wins by casting Synthetic Destiny OR Mass Polymorph

Requires: Synthetic Destiny OR Mass Polymorph in hand. 2 creatures (usually pilot tokens made by Shorikai) on your battlefield. Leveler and Thassa’s Oracle in your library. 6 mana available consisting of 2 or 1 blue respectively.

Steps: Cast Synthetic Destiny OR Mass Polymorph. Letting it exile 2 or more creatures allows it to enter Leveler and Thassa’s Oracle from your Library because they are the only 2 creature spells. Let Leveler enter the battlefield first, exiling your library. Let Thassa's Oracle enter the battlefield next. Your devotion is greater than the number of cards in your library, so you win the game.

Primary Win Combo Crisis Management: If Leveler or Thassa’s Oracle leave your library that’s a problem so there are ways to put them back but hold onto them for a while because you might draw an alternate win combo before you draw Synthetic Destiny or Mass Polymorph.

The way to get the creature win cons back from your hand into the library: Tutor for Dream Cache.

The ways to get win cons back from the graveyard into the library: Academy Ruins for Leveler or Hall of Heliod's Generosity for Thought Lash. Only Devious Cover-Up can get all card types so don’t use it as a counterspell unless that is your last resort to avoid a loss. There are tutors that can get Devious Cover-Up if it comes to this.

The ways to get the creatures back from the graveyard into your hand: Use Haunted Fengraf, Buried Ruin or Conqueror's Galleon (transform) to get them back into your hand if they get milled because you can still win by playing the two creatures directly from your hand together or with an alternate combo piece.

Alternate Win Conditions:

Obviously if you have Leveler + Thassa’s Oracle you can play the win combo directly without waiting for Mass Polymorph or Synthetic Destiny or any alternate combo that does the same thing:
Leveler + Jace, Wielder of Mysteries
Thought Lash + Thassa’s Oracle
Thought Lash + Jace, Wielder of Mysteries
If you have Leveler and Fractured Identity you can play Leveler then Fractured Identity on it to exile your opponent’s libraries then simply pass and they will all lose the game as they reach their draw steps. Important: Make sure you’re not the monarch or you will have to draw at your end step first.
Use Isochron Scepter to combo Dramatic Reversal for infinite mana and infinite untaps. This will empower your commander Shorikai to draw your deck until you draw another win option or required recursion.
You can IsoRev Blind Obedience to kill everyone.
If all else fails smash face with Shark Typhoon and Divine Visitation because 68 of your spells can make flying sharks with strength up to 8/8 and Divine Visitation turns all of your pilots into angels.
In summary the win cards to watch for are: Synthetic Destiny, Mass Polymorph, Leveler, Thassa’s Oracle, Thought Lash, Jace, Wielder of Mysteries, Dramatic Reversal, Isochron Scepter, Fractured Identity, Blind Obedience, Shark Typhoon and Divine Visitation.

Other important notes: The best way to keep Leveler and Thassa's Oracle in your library is looking ahead and shuffling if necessary so if you draw a card that can make you shuffle or put one back, hold onto it while you use all your ways to scry and look ahead of your draw. If you see them coming then good chances are you have a card that can move them to the bottom of the library and if you don't then make yourself shuffle it.

Also remember that counterspells are fun and useful but they are primarily in the deck to protect your win combo so save a couple even if your opponent isn't a blue control player because all colors can attack your win combo for instance if a black player muders one of your pilots in response to your combo then you can't get both creatures out of your deck anymore and it has a 50% chance of killing you.

You have 2 transmutable cards and they are both in there to act as tutors. The counterspell one will let you get a piece of a win combo as some of them have 2 mana cost. The land one that lets you transmute for a card that has 0 mana cost is there to get Pact of Negation.

The board wipes are there to stall and defend while you assemble your combo.

Your commander dodges most commander removal that opponents bring because he isn't a creature unless you crew him so don't crew him. Fighting isn't his job. His job is to draw your deck and generate tokens.