Thanks for the advice, kind words, and especially the edit MLC.
The rocks are very dull.... I'd add some highlights.
You'll want to make multiple instances of things, look at the top of the hill (unforested), It's very easy to see the pattern, and that's very bad.
The grass is very splochy, you might want to make it a little cartoon-y-er.
A good way to improve readability is to add in shadows. Good luck, chap.
Point taken on the rocks being dull. The palette (and the way it's applied) does suffer from some low contrast especially on the rock tiles. The palette on those probably needs a bit more range in value to fit in with the rest of the tiles. I like the highlights you did in the edit, but I'm not sure they work with the particular feel I was going for. The color and the positioning of the highlights on the edges between planes reads as glossy, wet, or almost glass like. However, although I don't have much time left for this project I may add another face/facet to the rocks that use a brighter color than the brightest on that ramp because I (think I) see what the point behind your advice.
On the alternate dirt tile: always good advice.
On the shadows: That's always good advice and if this was a static image (like the demo image instead of a group of tiles) I would definitely add them. I had considered doing a shadow set (of 50% alpha dark blue or black) for each tile. Unfortunately, because larger tiles (like the trees) and the nature of isometrics itself, the problem gets huge really quick. In the worst case, I'd be making n squared shadow tiles (where n is the number of tiles in the original set) because I'd have to project the shadow of each tile and curve or adjust that shadow onto every possible tile the shadow would fall onto. Practically, tho, it could be cut down by using more primitive shapes so somewhere between n and n squared - still too much to do.
If there's an easier way I'd be glad to know it.
I have very mixed feelings about the palette of the grass. On one end, it's smooth and soft, and looks nice... on the other hand the red is almost glowing it feels like. It almost makes me think the grass has a radioactive quality to it. Perhaps change the red to a soft blue-green tint instead? The variety and things you've covered with these tiles is pretty impressive, and it all comes together in a nice way 
I agree though, some contrast might do this piece some good(and I don't mean just ramping up the contrast, add some darks between the cracks of the rocks, and some highlights). Everything right now seems midtone... though adding such contrast might ruin the feel.
The flora, however, don't mix. Your palette jumps far too quickly to a few putrid shadow entries, and they have noticeable outlines. The trademark of the rock and ground tiles is the low contrast, soft faded hues, and absense of outlines. I like the grass splotchy!
So, my aim was to have background tiles err on being too low contrast to keep them in the background. For the plants, I was going for a bit more projected out into the viewer (because of their 'individual height' - if that phrase makes any sense) by giving them a small colored outline. I did need them to be somehow stylistically separate from the 'terrain' tiles. I had heard that outlining an object can be a good way of moving an image into the foreground.
All that being said, I agree I lost consistency in some areas (especially in the smaller broad leaf bushes v. the junipers). In the case of the rocks I think it went overboard and you guys are right that they need more contrast. Looking at the red again it does look a bit too much.
So:
I darkened the lower range of the rocks and lightened the upper range. I desaturated the red/dirt ramp (probably most noticable - at least to me - in the river banks) and darkened the deepest shades on the juniper bushes (the ones with the blue dots). The pine trees are recolored into a full green to get rid of that washed out brown.
Any better? Any more unified?
I should also note that the scale on these is roughly what's used in these sprites here:
http://www.wayofthepixel.net/pixelation/index.php?topic=4934.msg59827#msg59827if not a bit larger(?).
