So I would build your core around cheap-to-cast creatures with Shadow (can't be blocked by any creature without shadow, BUT also can't block any creatures without shadow) and other cheap "can't be blocked" creature options.  They don't need any extra cards to make them unblockable, so they're easy ninjutsu targets.  Plus they can be enchanted or equipped with cards that trigger on attack or combat damage, or be targeted/encoded by spells with cipher.  Obviously, enchanted/equipped/encoded creatures are not the unblocked creatures you'd want to also target with ninjutsu, unless necessary, but there are 10 creatures with shadow that cost 2cc or less, plus five 1cc creatures that are unblockable, so they make a nice cheap core to work around, and likely will help you start the game off fast.  This does mean a lot of cheap creatures you can't block with, so using ninjutsu to swap in big blockers with ETB/combat triggers will also be crucial to get blockers.

The unblocked creatures you will be re-casting all cost 1-2cc, and the ninjutsu cost is 4cc, so to really maximize the value of Satoru you should be swapping in creatures that cost 6cc or more.  The more it costs, theoretically the more value your are getting.  This is another reason I recommend Eldrazi creatures down below.

There are triggered abilities flying all over the place with this deck, so being able to copy them can help a lot.  Satoru's last ability is triggered, so copying it lets you see three more cards and keep another creature, as well as copying any of the ETB triggers you're getting.  While ninjutstu is an activated ability, it doesn't look like copying it will do anything, and there aren't enough other creatures/permanents with activated abilities to justify adding anything to copy them.

Since ninjutsu via Satoru costs 4cc to use, ramp is going to be a necessary element in order to keep things flowing smoothly.  I would say build around a core of 35 lands (you are mostly casting cheap creatures), and probably 10 extra sources of mana ramp (probably mana rocks). 

Draw is easy in blue (lots of cards that trigger on combat damage to opponents) so I would recommend having about 10 solid draw cards, ideally that will each draw a card (or more) for each mana spent to cast the spell.  The faster you get to ninjutsu-in your biggest/baddest creatures, the faster you can try to secure a win, so seeing lots of cards fast will only help.  Unfortunately, some of the best draw cards in blue are not exactly cheap to purchase, so hopefully I found/provided enough other options to get the job done well enough.

Your creatures with ETB triggers benefit from being flickered, so instant speed flicker spells will both help you get a few more ETB effects on the stack, but also allow your creatures/permanents to evade targeted removal (unless needed, I would hold such instant spells for protecting creatures).  While there are some beefy creatures with combat damage triggers that should certainly be in the deck, I think it might flow better if you go heavier on big ETB creatures and flickering, as they often swing a bigger punch (typically only getting one use per [expensive] cast).  The more I think about it, there seems to be two different directions to take this deck.  On one hand you can go flicker-heavy and saturate the deck with big ETB creatures.  On the other hand, you could go with more combat damage triggered creatures, and add in more ways to keep making them unblockable.  The two decks might only have 15 different cards.

Also take note that an unblocked creature with first strike or double strike can deal first strike damage, then be swapped out with ninjutsu, then the incoming creature will deal damage in the regular damage phase as well.  As such I've added a few creatures with first/double strike to the list, but I tried to make sure they had flying or some other form of evasion.

Some creatures are worth returning to your hand from play to ninjutsu back into play again to get their ETB or combat triggers again, so there are some options added to the list to give you that option too.

The Eldrazi creature options don't really jive with ninjutsu, because you're missing out on the cast triggers and most also have attack triggers you won't get until the next turn either.  BUT, you are cheating in high-casting cost and devastating creatures for 4 mana... I would honestly lean heavy on anything with Annihilator, as those will allow you to greatly hinder anyone who is getting too strong on the board.  A turn 4 It That Betrays is hard for the rest of the table to recover from without targeted removal coming soon after.  The prices vary, but plenty of good Eldrazi are below $5, so it would be easy to load up on a bunch of them in a budget build.

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Fun cards....

Dusk Mangler won't be cast when you ninjutsu it in, so it has no drawback this way.  Great flicker target as well.

Predators' Hour is fun in here!  Lots of unblockable creatures each triggering this = a big pile of exiled cards you can play for the rest of the game, and spend any color to cast... I mean... WOW... for 2cc... and currently less than $1!  (Also, if any creatures you ninjutsu out have first/double strike, it'll trigger twice, once for them, then again with the new creature's damage.)  Predators' Hour allows you to play lands from its exiled cards, so there's a small "ramp" benefit as well, letting you hit more land drops.  In this deck it has tons of value for 2cc.

Blade of Selves on an unblockable creature = multiple free tokens for ninjutsu targets, assuming you have enough mana and creatures in hand to bring in.  But you don't have to re-cast your creatures, like usual, so it's saving you 1+ mana every turn, on top of the creeature token copying shenanigans.  This is a must have in an ETB build, as Blade of Selves can make things crazy on something like Ancient Silver Dragon of Archon of Cruelty, or maybe Astral Dragon...?  But take note that any creature that triggers on attack will not trigger with token copies made by Blade of Selves... they are not declared as attackers, so they don't trigger... so no It That Betrays, sadly...