Positives

Love the little speech bubbles that show what they are thinking.
Love the relentless perusal the AI has even trying to cut you of forcing you to be careful.
Loved the fact that when I hurt an enemy saw him have some food.
Loved the branching pathways that allow you to chose routes.
As I said before the core gameplay is very fun and solid and the little touches mentioned above really give the game a depth and charming personality.
Issues identified

Two songs playing at once happened when I manage to escape perusing ninjas action theme continued and stealth music started playing at the same time.
On level one on the high platform before the bamboo prison grabbed the edge and tried to use the intact button to hide in tree foliage character froze or I could have been wall climbing/ jumping character looked compressed like when ducking (unable to do anything)
Checkpoint on first level hard difficulty sporadically doesn't work, instead screen pans down at start of level on first hint guy repeatedly, going to last checkpoint in menu results in same if that is the case. Also case with third level (it's tough doing it in a single run) probably the second as well but had an easy run so can't yet confirm.
Saw one samurai running into a wall to try and get me while I was above them.
If enemy is in throwing line of site for item should hit them rather then go through them. Maybe i was at a bad angle but seemed like some of projectiles went right through them though it could be I was over estimating the range.
Suggestions

When using the stun grenade throwing the last one automatically cycles to the next item, it should remain on it so can use alt function immediately.
Seems strange when an enemy see you in the water will jump in to there death rather then pelt you with rocks. Falling down pits i understand more.
On hard when you re spawn at a checkpoint on hard it shouldn't restock all your items, remember which ones you have used.
Addition Suggestions

I am aware it is a very early alpha however I though of some potential additions if you have the time.
Ninja rope that pulls you up to higher platforms, vines on the ceiling ( like the rope from the worms game).
If you are spotted the enemy (maybe a specific one) pulls out a horn that alerts and makes all surrounding enemies come the immediate vicinity, area of effect could be indicated in a similar manner like Taros special ability.
This would be more complicated but samurai can throw/place little lights/flares/lanterns in areas you have been seen when you extinguish torches which you can also extinguish.
Could put a timer on levels to enable potential speed running. With platforming challenges are you planning to have them timed?
When falling to their death the player character could say something witty in a dialog box
I also have a curve ball idea with another game i supported Ninja Pizza Girl http://www.disparitygames.com/ninja-pizza-girl/ maybe you could do some cross over content like a costume?
All that said I am really enjoying it, and a lot of the issues identified are from it being such an early build. I can really see the passion you are putting in the game

