I do agree that Lightning Main's kit is a bit over powered, not necessarily the one skill. With just a few ninjas you can make a investigating blitz team or a CC resisting sword team. Those 2 teams pretty much counter most teams. The fact that one main counters all mains is in need for a nerf.
On the other hand, the shield mystery for fire main is fine. You talk about how clearing all debuffs is broken, well just look at Gaikido Pain which does the same thing before every action to your team, or Hanzo who does it to your entire field! In an average fight a Fire Main can get the shield off about once, which I actually think it needs to be buffed to a 2 turn cool down. Now the other part you think is op is the immunity, but look at there are ninjas that have that built in plus Lightning main can give that to 3 sword ninjas. The shield skill is fine