Hey nice piece. I've read nothing so forgive me if I'm being redundant but judging by the last version (which is good, again), I have the feeling that:
1-You're not making the most out of your own palette.
2-You could make some lines more appealing.
3-You could make some clusters more appealing, too.

I played with your pic just a little bit to strengthen my point and -hopefully- help you.

Just being playful, changing some clusters and curves to make them more appealing to me, fiddling just a little bit with your palette and adding some AA here and there. Nothing is a definite statement, just some food for thought!
 
So...
For point 1, you already have the colors that are needed to make things a little bit less rough (with AA) within your piece. Antialiasing is a delicate task because overdoing it is bad (and can be worse than not doing it at all). But you did some AA. So, why stop so early and end up with rough edges? Especially since your piece is an illustration, and more so, an illustration based on a photograph. If AA is not the right way to go here, I do not know when it is!

For point 2, some of your curves could respect the pixel art 1-2-3...3-2-1 rule a bit more. I mean it's okay to not respect it all the time (especially if you antialias it) but it's something you should keep in mind: a more encompassing gradating curve feels more appealing than a varying one (like what I did for her left shoulder).

For point 3, kinda same thing but even harder to explain. Really look at all cluster and judge it. Is it really the most appealing you can make? If not, try to change it a little bit. It's often about simplifying it, making it more round and soft or on the contrary, more pointy, depending on the context. The key here is to step back from actual anatomy and go into abstraction. Try to think in terms of pure "shapes" and the solution will often appear to you.

But clearly, seeing the awesome progress during the whole thread, you're totally on the right way to go!

Nice, everything is kinda here. Just require a little additional polishing.

Here's an attempt of mine:


What could help you improve your piece:

-Be more consistent with your pixel work. Hard to explain that one but everything should look tight and intentional. Maybe this part comes with millage... I mean you really have to think about what you're pixelling and be procedural about it. Even if it's a micro crevice in the rock, it starts somewhere, ends somewhere, it's affected by light and should be antialiased in a controlled and consistent way. You have a tendency to harshly break lines for no valid reason, for instance.

-Avoid things that do not work visually. You should work with the pixel contingency, not against it. Sometimes pixels are too big or too small to represent what you want. In such cases, GIVE UP and WORK AROUND, do not try to represent it in a way that does not work. Here I'm talking about your very small floating rocks. It's almost powder or something. It will not work in front of a background or within tileset. I think it's better to make them bigger and with a similar style to the bulk of the rock. It'll convey the same idea of "this rock is magical or something" but in a more clear visual way.

-Spread your values enough. Here your darks are too close to each other, a light dark can be TOO dark and become counterproductive within lighter areas for antialiasing. It will make a harsh staircase effect instead of smoothing things out which is the opposite of what you want. Here I'm talking about the lower-right part of the upper rock. It's almost like your AA is making things worse just because the light dark is too dark.

-Maybe, make your greys more interesting by coloring them more + ramping them with a hue shift. I made something from bluish darks to yellowish lights but you can do anything. Yours are a bit yellowish and it's good but I thought it was a bit too timid and unsaturated.

-Aim for tridimensionnality even more than you did. Work from simple to complex. Start really simple and geometrical and only then, add a controlled amount of gritty details. Think "edges and planes affected by light" even more. I did not put an emphasis in my edit in order not to modify your piece too much but keep this in mind, it'll help you with rocks.


Oh and I think your bottom part looked weird because it was not geometrical nor rocky enough. It felt unnatural for a rock, even more for an old megalith. If you want your rock to be smoothly grounded, maybe do it with additional soil and grass but not with the rock itself.