I don't know if TTV's made up their mind about this, but I feel that the presence of Stone as a separate element from Earth is something which should go. Before you just say "no," please hear me out.
I know that Earth is defined in G1 as just soil and dirt (which is kinda lame when compared to things like fire and rocks, but I'll put that aside for now), but the thing is, Toa of Earth, by necessity of being cool and working with their thematic element (pun actually not intended for once), must be able to create earthquakes. This was a thing in G1, and it's obligatory for any other adaptations. However, let's consider what earthquakes actually are: movement of tectonic plates, which just so happen to be made of rock. But if Toa of Earth can cause earthquakes, which entails controlling rock to a degree, then what separates them from Toa of Stone?
This argument is not rooted in advanced science, as we're dealing with a fantasy franchise wherein the laws of physics must not have any relegation. This argument is based on the fact that one type of thing is made out of the same type of stuff as another thing, leaving the only difference between these two elements being...location? It's one thing when it's like Ice and Water, which are in different states of matter and have different properties and applications. However, we're just talking about hitting people with rocks in different ways; not stabbing people with water versus throwing them around with liquid. Pohatu, therefore, is just redundant to Onua in terms of powers.
I know that there are arguments for keeping Stone. The one I've heard most is that Stone is cool as a thematic power. This is true, but it doesn't have to go away, just be used by another type of user. Stone just doesn't really add anything when Earth could--and should--possess the attributes of that element. Or vice versa, but when dealing with elemental powers, most works just use "earth" and not "stone."
Another argument that I've heard is that, like Lewa's change to a Toa of "JUHNGOLE," it would be a pointless shift from that which is already established. However, Lewa's change added nothing. It didn't make more sense on a thematic level, it didn't fit his character better, it just sort of happened. That's why it was a bad change. If Stone and Earth merge, and Pohatu gets a new element, then that enables the character roster to have more thematic components without losing any, while at least some logical headaches of the elemental roster are done with entirely.
Lastly, I've heard that the elements don't really need to make sense, or that overlap between them does not really have any detrimental effects. Here's the thing, though: if the elements are not clearly defined as being different types of material, then why classify them into elements and not just magic? "Elements" entails distinction between the objects manipulated by the user. If two beings with different elemental powers are controlling the same stuff in different places, but can only control that stuff when it's in their relegated place, what's the difference?
As for what should replace it, I'd personally choose Iron, but maybe you guys have a better idea. That's really my thoughts on the subject, and not a definite answer. There are probably other arguments for keeping Stone, and if there are any which justify its existence, then do put them forth.