Chakra cost is also used to determine who Auto will use first. I have a Position 1 J-Minato, and a Position 2 Shisui. When round 2 comes, Auto will choose Shisui over J-Minato, as while both provide a method of interrupt, Shisui costs 40/40, while J-Minato costs 20/40. This may seem good on paper, to make "full use" of all available chakra, but this does lead to bad mystery timings (Like if your Pos 1 is faster than the enemy Pos 1, but doesn't get selected, so your team suffers thier Pos 1's nuke first). Personally I wish Auto took Position into account over chakra cost, as clearly a Position 1 would be prefered over any later one.