Every build has it's weakness. Like some have stated above, Lightning teams tend to be Blitz teams. Most are not set up to handle much after round one and two. However, even at that, they are not with out a weak point. Root of the Warrior only effects 3 ninja. Watch at the start of battle for who isn't buffed (if there are 3 sword users) or the non-sword user, and attack them round 1 and two if able. Even if most of the combo/power comes from the 3 sword ninja, taking out the 4th Should make it a 3v3 on round three. This is also when their buff is gone, so you should have the upper hand.

Also keep in mind, some ninja have the ability to remove buffs, including Root. Mifune in slot one (as long as your faster) on the enemies highest target, along with a CC combo backing him up means you just took someone out of the round for the Lightning main. When that happens, they tend to fall apart because their team is not set up to counter that when it happens.

Problem is this is too easy to counter. This was the "meta counter" team some people on my server were running before 2.0. It was ok for the Fire Main/Tobi teams that counted on the ignite buff/debuff. But it fell way short against any other team.

On my server (high level play atleast), most teams run some sort of of round one CC/interrupt (Iruka, Earth/Lightning/Fire main, Ao, etc.), along with a CC of some kind in the chase. You know he is going to use Sasuke or Jugo round 1, so be ready to counter it. Then in round 2, thanks to Kimimaro almost always being in slot one, you are free to use Your combo starter to counter the Lightning main (cause as long as you stopped Sasuke, that is all he c*e). Round 3 sees Kimimaro move, but at this point you should have killed someone. If you don't care about trying to stop the Main, aim for Sasuke, as he dies really easy.

Or as I said above, run Mifune in slot one, and you get that free move round 2, and can control the main with a CC combo. I think one of the other Mains even have the ability to do this.