I know I have been silent but If I may.  I believe that the powers issues could be solved in game.  Being thrown into other dimensions is a great explanation why my shinobi would at first have trouble even channeling his chakra.  At first, the mechanics might back fire or be null for some of my Jutsu until I am able to find balance.  The same could be true of other powers except for weapons and such.  As we move through the story we can finally use some of our powers or perhaps even find substitutes.  

Second, being in an unknown world has its own challenges.  Society and its rules are completely different.  We will not be OP so we will have to be careful not to upset the order and become targets.  Even if we were to kill without discrimination this could have an impact on the story line itself. 

Finally, I think that it will be fun to see the dynamic of the group.  Establishing a structure is always hard especially for people who may be solo or have  differing views.  While I do believe that goals and end states are good to think about. I don't see them as completely necessary to move forward. 

just my two cents.