Well that's only if you look at nature advantages by themselves. IIRC, if a water and a fire jutsu strike w/ about the same power in both of them, we are led to believe that the water jutsu will overcome the Katon. If the same happens between an earth style and a water style jutsu, the water jutsu will inevitably fail unless it's a special circumstance. So overall it's fair and balanced. The only real way I can see it being unbalanced is the idea that there aren't as many fire style users in the NU as earth style users.
In the end the nature advantage is only worth taking note on in certain fights. Do most of the Konoha Rookies even use an element when fighting? By strictly feats, water style is actually really versatile. Even w/o KG usage. Water clones, water projectiles, pressurized water prisons, and a blinding mist were all benefits that Zabuza got without a blood line! Of course I assume that water ninja are better when water is already present.
I could be getting the entire idea of your thread wrong but meh