Now I have to admit this game isn't that hard but there seem to be a lot of spots that I got stuck.  Often it's very clear I'm missing some not so obvious action to advance.  I have completed the game and think I've been stuck on almost every level after the first two.  In search of finding a solution online I've found several forum post about people getting stuck.  Here is my list of areas I got stuck and here's my solutions.

In School Invasion I was stuck for a while at the point you have to close the gate.   What happens is several ninjas come at you when you try to close the gate.  I thought I had to kill all the ninjas before I could finish closing the gate (two levers to pull down).  So I'd pull one down, kill the ninjas then do pull the second lever.  Problem is if you take too long more ninjas come and lower the gate again.  What I didn't realize till was I can pull both levers and ignore the ninjas to close the gate.

In Okiku's story I got stuck twice: once at this point where I needed to throw the robot ninjas and again on the boss for this level.  Towards the end of this level you need to pounce on the robot ninjas and flip that at this giant machine in the middle of the room.  The robots will explode and after you've got this three times your good.  This is one of many encounters where you have to perform a specific maneuver to progress.  You need to block the attach than hit jump which will allow you to throw the robots at the machine.  I never used this technique after this encounter.

The boss at the end of Okiku's story is the flame thrower guy.  This guy is crazy annoying but easy to beat if you just use the dash attach on him.  Just dash in then dash out and eventually this guy will runaway.  All other attacks seem to fail against this guy.  He is extremely cheap as he will one hit kill you if you get too close when he does if fire jump.

On the very next level I got stuck trying to cut a rope.  On the Lowdown East Pass level you need to cut several ropes to maneuver the multiple parts of a statue.  One of the ropes requires a vertical slash in focus mode.  The others you cut don't and there is no hint you need to perform this specific sword maneuver.

The final boss for the Lowdown East Pass happens to be the flamethrower guy again except this time he's got a rocket launcher.  To beat him you've lot to slice the rocket he shoots at you.  To do this use focus, hold the vertical sword attack button down and charge up the attack.  You'll see a light at the end of your sword when it's ready.  Do this a couple times and your good.

On the Doppelganger level I got stuck when I found the wild five.  These samurai are very hard to beat but what I did  was block and kick until I had over focus available.  Once I activated over focus I was able to slice them up and move on.  Some people had difficult with the boss on this level but I found him easy if not a bit long.

The next level is Kuma's story which isn't hard but does take some skill and determination.  There are no secrete moves to defeat him but  spamming your heavy attack sure doesn't hurt.

On the Empty Seven story I got stuck twice.  The first time was when you pull down these three levers.  It took me a while to notice the wall moves at the top of the stairs so you can jump up and progress to the three distinct battles.  I then got stuck fighting the Empty Seven with the gold arm gun.  You need to enter focus mode at deflect the bullets back at him using X. 

The last spot I got stuck on was the final boss fight against Justice.  The middle encounter against him he shoots these tree like arms from underground at you.  I knew I had to cut those I just didn't know how.  Turns out you need to enter focus mode and perform a horizontal strike.  After this you need to fight him like normal and eventually you'll take him down.