I've heard that. A lot of people told me it's very good. I might watch it when I have some time.You should watch it , its really something else.
Take Goku and Naruto characters as an example:
Same energy concept would negate all of Goku's attack ( Energy absorption via Rinnegan or Mokuton or whatever ).
Not to mention Genjutsu.
In other words , your same energy concept doesn't resolve anything , so you should leave it as that. ( it's called a cross over battle for a reason )
But those that you described are the character's ability. He has the ability to do that, so taking it out doesn't fit the main idea(comparing the chars abilities, skills and powers).
And that doesn't negate all of the atacks in dbz. They still have physical atacks, not to mention that they can take advantage of the shockwaves and explosions done by their ki blasts(Explosions and schowaves are made of thermal energy, or cinetic energy, and not by ki/chakra, so rinnegan users or moktuon users wouldn't eb able to absorb it).
The same idea of the bijuu dama.
The system allows the char to use all of thier abilities.