Let's rewind to the point.
Evolution of major traits (such as the ability to use Elements) doesn't work on the scale of thousands of years, it takes millions of years. It doesn't seem likely that the animals of El Nido would evolve this quickly.
Hmm, guess I didn't spell it out well enough there.
If elements were new, (introduced at most 10,000 years ago), the animals wouldn't have enough time to evolve to use them.
If elements were natural, animals would have had millions of years to evolve to use them, which would explain why we see animals using them in Chrono Cross.
The possible flaw in this theory is that we never use of elements in CT. Perhaps they were used, but Crono's party didn't recognize them as such. Or, there's that wierd "Lavos sealing the Elements theory" that doesn't even make much sense to me... Crono & Co. not identifying them seems more likely.
Now, in the defense of the altered laws theory (which is starting to seem like a reasonable way to wave away the difference in game mechanics between CT and CC). Given our lack of understanding of the true laws of nature of this world (we lack the ability to experiment as I'd prefer), we can't really say what's going on, but imagine this model:
We have two "Planes" to the world: The Material Plane and the Mana Plane. The real world exists in the Material Plane. The Mana Plane is mostly a miasma of elemental energy (originally Fire, Ice, Heaven, and Shadow). When someone uses magic in any way, they draw the element(s) they need from the Mana Plane, and do whatever with it. These elements pervade the Material Plane, and slowly seep back into the Mana Plane to maintain equilibrium.
What would happen if new elements were released into the Mana Plane according to this model? Well, the Mana Plane's only contact with the Material Plane is when magic is cast, so it would have no initial effect. When Dragonians use their Yellow and Green Elements, Yellow and Green elemental energy is released into the Material Plane. As I said before, eventually, its concentration in the Material Plane will build up enough that people with Yellow and Green innates appear.