1. The nice thing about a checkerboard dither like this is it doesn't get repetitive, because there aren't really distinctive elements to it. However, some of your cloud dithering employs high-contrast colours and stands out too much. You have some intermediate colours available from other parts of the image and could use those to make the gradation subtler. Dithering high-contrast colours tends to look noisy on modern screens, so it's best to keep the contrast low, or to not dither at all.

2. Having some empty space is good. I think you actually need more of it, not less. Right now, almost every part of the screen is competing for attention, there aren't clear focal points (I'll address this later in the post). The bottom right area could use some faint, subtle detail, like some faintly highlighted foreground terrain. You could also move the title down a little, so it overlaps both the black and pirple areas.

3. The text placement looks fine, though I'd move the buttons further away from the edge. Try to keep a large margins around the edges of the screen where there are no important elements, give your text room to breathe. Large margins make things feel less claustrophobic, and keep the player's eye on the screen instead of letting it wander away.

4. I agree that you haven't quite achieved scale. This is for two major reasons:
a. You're not employing overlap, so it's not immediately clear when things are in front of other things as opposed to just below them. Instead of the foreground character being contained entirely within the purple, let them overlap the mountains and horizon, etc. Let the city overlap some of the clouds. Overlap creates depth.
b. The atmospheric perspective (things being more faded the further away they are) is very weak, which makes the distant objects look closer and smaller than they're meant to be. The clouds in particular have very high contrast that makes them look close to the viewer rather than far away, and this contrast is also very distracting. The clouds stand out more than the character and city do. These contrast problems make it unclear what the focal points are, and draw the eye to the wrong parts of the image.

Here's a messy edit:

The big changes:
Moved the character and city over so that they're on opposite sides of the image, which creates distance and tension, implying the character has to brave the distance to get to their goal.
Lightened up the city and mountains (more atmospheric haze), which makes them look further away. I used the previous mid-ground terrain colour to add another "layer" of mountains between the city and the foreground, which helps create more distance. I also reduced the contrast in the city, as more distance = more haze = less contrast.
Reduced the contrast in the clouds (mostly by getting rid of the darker shadows), again to add the look of intervening haze that makes the clouds look distant. I think they could be made even hazier, mine still feel rather close.
Changed the various foreground and midground layers to be more diagonal rather than horizontal, diagonals look more dynamic. I also made the character overlap a mountain valley, so they have a lighter background, making them stand out better. This also lets them overlap a bunch of colours instead of being contained within a single colour that makes them look caged in and static.
Added some faint lighting to the foreground and midground terrain, which gives it some volume and helps sell the distance.
Moved the text to have bigger margins and to work with the adjusted composition.

I think the scene still feels a little bit flat, mostly because of the clouds. Clouds in the foreground could have some shadows this dark, but most of the clouds should probably be further away and have less contrast.

Raising the window works!
The original looks strange because of the perspective, I think. The bottoms of the "legs" of the arch both have perspective that suggests a higher camera/horizon, which is why they look a bit strange. Having the centres of the "legs" not descent so much compared to their sides should help create the look of a lower camera.

Nitpick: I don't think you need the dark line on the horizon, it looks cartoony compared to the rest of the art.

Where is the light coming from? Different parts of the character appear to be lit from above, below, left, front... A stable light source should help you with conveying the form of the character, and may even help add in those gelatinous blobby shapes through some subtle shadows.

I'm not familiar with this character, but it seems the red gem/eye is positioned very differently in your version from the ref?

Many games cheat and make the openings artificially wide so that you can see the floor in the doorway instead of bothering with getting the size of the door correct. Some don't even bother with the concept of side-wall height and just have the doors be a simple break in the top of the wall, no indication of wall height. Many other games just don't bother with east/west doors at all, and instead just have north/south doors linked up by wide east/west hallways (e.g. Sword of Mana's Vinquette Hall), and it's a convention most players don't mind by now.

If you don't want to do "cheat" like that, consider having lighter wood in the doorway, lighter at the bottom (where the floor reflects light most strongly at it) and darker towards the top, and perhaps some special tiles to draw attention to that area by giving it a more interesting shape (door frame, hinges, decoration, etc).

In general, you should rely mainly on things like silhouette, floor patterns*, open doors, other decoration, and light shining through the doorway to show the door is here. You might even benefit from not having the top of the door indicated with the break in the wall, since it's a distracting visual element that doesn't correspond to the walkable part of the door.
* By having floor patterns that cross the doorway (lengthy carpets joining rooms, continuous floor texture instead of borders like at other walls, etc), you can subconsciously hint that the rooms are linked in that area, so the player doens't even "see" the wall between them.

An unrelated thing: Your walls feel very flat because the wood is perfectly aligned with the stone and plaster/daub, looking more like a wallpaper with those things drawn on rather than actual structure. Letting them stick out would help with that. You don't have to break tile boundaries, you could have a couple of pixels of wood/dirt/dark-dust at the bottom of the stone or something like that.

Here's a fairly minor edit:

I gave the walls a bit more volume by raising the stones a couple of pixels, and added sticky-outy bits at the bottoms of each pillar. Those same sticky-outy bits are visible around doors. I made the rugs less brown (so they don't blend visually with the walls; they don't have to be lighter, I just used the available non-brown colours)  and extended them so that they look more like rugs laid between rooms, rather than just something attached to walls. In the back room, I also "opened" the door. I got rid of the tops of the doors, since they weren't conveying useful information imho, and were just "lying" about where the door is.
This is still not as clear as the north/south doors, but I think it reads better than before, at least to me.

Something missing from my edit is a distinctive visual element for the doors. For example, what if all the doors had little awnings, or some sort of supports, or other bits that stick out and look similar in both front and side view? Those would help a lot.