As for me, Im fairly ok with how it matches me, but I was simply shocked to see such a difference in damage that the enemy dishes out and receives from me if only the base stats are used.

Hello, it is not only the base stats you have to look at but sage naruto especially. His mystery does 2 times dmg, plus repulse damage resulting in triple dmg. If it crits, it will deal even more dmg, even more so if you are lightning since wind is strong against lightning.
So indeed, no wonder he took 2/3 of your life.
base stat for elemental disadvantage is -20% which is alot. So by default wind will deal 20% more dmg in general to lightning.

Alright, here's the deal, I really don't think its only the base stats, I didn't take a screenshot, but:
I met a team, thats exactly the same as mine, except Darui is replaced as Kimimaru.
My power is near 44k + I had a barrier running from Darui.
I asked my opponent, he said he had "Near 49k"
In either case as far as Mifunes Ult goes - its not affected by the barrier.
My power in arena was 26642 his was 267* (dont remember the last numbers).
His mifune dealt a bit over 50% to my main, mine did just a slight bit under 20% (maybe 20%).

I would expect these numbers in real life, but not in arena..

the numbers are sometimes randomized, i have seen my ninja deal 700 damage 1 turn,only to deal about 1400 the next
it could have been that