I'd like to see the shared timers of Yonin/Innin removed and brought in line with the 1 minute timers of Seigan/Hasso.
Ninjas being quick and agile should be able to react offensively and defensively according to the current situation. This simply isn't possible with a 5 minute shared timer.
Samurai are able to switch offensively and defensively on the fly. I believe that Ninjas should be able to do the same.