I have just downloaded the mod yesterday after a few months break playing the M&B. The mod is awesome - especially animations. And it is not bugged like other modes (Shogun). The choice of weapons is awesome: I like O-Dachis and Ninja armor - and here they are. So first of all thanks for the great work.
But since I had a lot of experience playing other mods, I would like to share my thoughts on the possible improvements:
Realism (I know it is rather a cinematic mod, but this concerns fighting mechanics):
1) Shurikens overpowered (both range and damage). Originally this weapon is not designed to deliver lots of damage, but to cause pain and destraction.
2) Connected to the first one

- the scripted injury shock would solve the problem. When the enemy recieves lots of non-lethal damage he is likely to be stuned for several seconds. Would be nice for the non-lethal katana strikes too, since this looks stupid when you deliver the swing to the opponent's body and he continues atacking you like nothing happened. This kind of injury was implemented in the 1866 mod for the first M&B - so that the bullet injury would stun enemies like in the films, when they got shot at and stay there looking where to fall down

. Fits with the samurai theme pretty well too. Just look for the proper code in the 1866.
3) Thrown wakizashi can't do more damage than a thrusting atack by it hand-held. This is just not right.

Lower the damage - it would still be beneficial to throw wakizashi if you implement no. 2. since it will stun the opponent giving you some time to get in close and finish him with the katana strike.
4) I believe, that the large (two handed only) swords are under-powered (those should by no means do less damage vs. naginatas ect. - since naginatas were designed as the cheaper versions of large swords). Maybe you can tweak this a bit to make them usefull - at present they are not better than the best one/two handed katanas, though obviously longer (which in my book means more damage due to the wider arc of the strike).
Shields:
Using off-hand katana and wrist-guard as a shield is fine idea, I love it. But those shouldn't block arrows. You can't block arrows with those really

And there were special shields to protect from arrows in Japan:
http://t3.gstatic.com/images?q=tbn:ANd9GcSM0riIs4Z8rHabkxlBwmZ8QfkxeW6E1NEwl2b1BY91gTmiG5vV
Here is the historical reference link:
http://books.google.ru/books?id=eyMYelZlKekC&pg=PA89&lpg=PA89&dq=medieval+japanese+shields&source=bl&ots=mqxAuufNZ8&sig=TlBlgqLqaq3npjev6EMvrykb5n4&hl=ru&ei=mppnTsrCJIzt-gawhfDuCw&sa=X&oi=book_result&ct=result&resnum=5&ved=0CEEQ6AEwBA#v=onepage&q=medieval%20japanese%20shields&f=false
Basicaly those are the tower shields used during sieges and large battles to protect from arrows. Those should really be introduced into the mod. Make them cumbersome, so that one would want to drop it as soon as he got into the proximity of archers, rather than carry it over the back.
Basicly that's it.

It would be nice to see the japanesse castles/taverns ect. instead of the european ones though.
Thanks for the great work again.