The Naruversity
Yeah earth and water jutsu do seem to have an advantage over other elemental ninjutsu types in that while they can be used to produce fake chakra earth and water, they mostly involve manipulating existing matter rather than producing a temporary chakra construct that mimics the properties of real matter. That's why Gaara was the only Kage able to touch Madara with his ninjutsu - the Rinnegan's Preta Path ability was unable to absorb his sand because it was real solid sand, while it absorbed both the Mizukage's water and the Raikage's lightning because those were chakra constructs.
I think you are correct about both explanations for the base 5/6 limit on element types. I think the Sage invented and standardized those 5/6 basic types, and the newly chakra using ninja stuck to those simplified teachings and were forced to use handseals for them all because they didn't *have* affinities yet. Over centuries of using ninjutsu the types of chakra they used started to affect their DNA, and ninja families developed affinities for the elemental types they favored. These new and growing affinities permitted them to invent new elemental training techniques that allowed them to elementally transform their chakra without handseals. Those 5/6 basic chakra types were used so widely that affinities for them spread into the gene pools for every nation, though they were still not evenly spread. (wind is rare outside of Sunagakure, and all of the 5 great nations still favor one elemental type over the others to the point they were named for that element)
Later on ninja started experimenting with new element types like shadow manipulation, medical chakra, toad oil, syrup release, etc. However those chakra types are much younger and the clans using them have not had enough time to develop affinities for them, so they haven't been able to develop nature transformation training for them. Because they cannot be used without handseals and they aren't widespread, the wider ninja world academia does not consider them to be "official" elemental nature types.
Yeah earth and water jutsu do seem to have an advantage over other elemental ninjutsu types in that while they can be used to produce fake chakra earth and water, they mostly involve manipulating existing matter rather than producing a temporary chakra construct that mimics the properties of real matter. That's why Gaara was the only Kage able to touch Madara with his ninjutsu - the Rinnegan's Preta Path ability was unable to absorb his sand because it was real solid sand, while it absorbed both the Mizukage's water and the Raikage's lightning because those were chakra constructs.
I think you are correct about both explanations for the base 5/6 limit on element types. I think the Sage invented and standardized those 5/6 basic types, and the newly chakra using ninja stuck to those simplified teachings and were forced to use handseals for them all because they didn't *have* affinities yet. Over centuries of using ninjutsu the types of chakra they used started to affect their DNA, and ninja families developed affinities for the elemental types they favored. These new and growing affinities permitted them to invent new elemental training techniques that allowed them to elementally transform their chakra without handseals. Those 5/6 basic chakra types were used so widely that affinities for them spread into the gene pools for every nation, though they were still not evenly spread. (wind is rare outside of Sunagakure, and all of the 5 great nations still favor one elemental type over the others to the point they were named for that element)
Later on ninja started experimenting with new element types like shadow manipulation, medical chakra, toad oil, syrup release, etc. However those chakra types are much younger and the clans using them have not had enough time to develop affinities for them, so they haven't been able to develop nature transformation training for them. Because they cannot be used without handseals and they aren't widespread, the wider ninja world academia does not consider them to be "official" elemental nature types.