I personally prefer Shisui with Lightning main, because of the root passive mainly. I'd put Itachi Anbu as position 2 as well in the case of lightning main and keep running the main support only. You could also use the reset passive if you want. Fire main does work excellent as well, could use the reset passive with him too. To be honest both versions are just working fine, it depends which team you enjoy playing more with.
Shisui is not the best ninja as you said in our me
Hope that helps and good luck!
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