Thank you all for the feedback, and thanks for the edit, Facet - that does look a lot better. I'm putting this on hold for finals week, but after that I'll pick it up again and rework things.

I like your dirt/stone tiles, but the trees look odd because they have very blue-purple shading when the rest of the scene does not. It's a definite improvement but consider the Secret of Mana reference images in the tutorial link, particularly the one where they first zoom in on the grass tile. The exaggerated shadows on the trees work there because the same shadows are used elsewhere in the tileset.

Your grass tile is bringing the rest of the scene down, I think: it's got very strong grid lines and appears to have been made with a noise tool, so it has extraneous colors in it. The same tutorial has a couple sections focusing on grass tiles and removing obvious grid lines, so that should help a bit.

The whole scene already looks much better than your first one! And I agree with Zizka, I like what you're doing with the house.

e: Quick 'n dirty example of purple shadows throughout the set

This looks much better already!

Your tall grass is really dark and heavily contrasted compared to everything else, though. I'd lower the contrast on that so it matches the rest of the set. I don't know if the shadows are mocked-up or not but you have some stray pixels in the shadows on the trees. The shadows on the flowers also seem too diffuse. Consider how close they are to the ground.

The "lightning bolt" coming out of the cloud is distracting, it kind of makes them look like thought balloons. It's not exactly bad, it's just kind of odd? The clouds also feel a little small compared to the rest of the scene, and I think they might benefit from another lighter shade. You have three colors in them right now but the two darker shades are close enough that it just looks like two colors.

The green mushrooms are also really distractingly bright - I'd tone down their saturation a little.

I'm picking over the details since you want it perfect, but your second mockup already looks so much better than the first. It's coming along very nicely. 

Thanks for the feedback!
Do you mean on the "background" bits of rock? That'd help break up the monotony.
I wasn't really sure where I was going with those blocks, I may remove them. I think the grey ones may need work as well - they were meant to be stone but they turned out too metallic.

And yes, there will be monsters! I'm still not quite certain what they'll be, which is why they're not here yet.