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1. More hotkeys. Ideally - a way to remap hotkeys to suit your needs. For now I really want to see hotkeys for zoom (Ctrl + and Ctrl -), scroll (horizontal scroll bar doesn't display for me in fullscreen mode btw) and view modes (full, cross section or depth). It would be even better if zoom didn't reset your view point to the center of the voxel each time btw. A hotkey to select next/previous color in the palette would really help with drawing textures, something like Ctrl + Mouse Scroll Up/Down, but I guess there's no such feature to assign a hotkey to. Would be nice to have one, it's easier than use a combo of darken/lighten and then eyedropper to pick the next closest shade without distracting to click on the palette.
2. Customizable colors or graphics for "selected color" marker (they can't be seen on some colors) and unique markers for currently selected color and used colors (only one kind of markers is shown at a time, so if you have "show all used colors" enabled, you don't see where is the color that is currently selected). Maybe something like on the picture 3: selected color and used colors are marked by different markers, and when one of the used colors is selected, they overlap and create an unique marker.
3. Customizable color for grid that is shown in "emphasise depth" view mode. Red color doesn't go well with housecolor and 200-203 unitem colors, being able to pick a custom RGB color for it would solve any contrast problem. It'd be especially nice to have a hotkey for this as well.
4. In "replace color" window, move the color preview (color that your mouse is on currently) closer the selected color preview, like it's shown on the Picture 2. So it'd be easier to compare the colors and pick the right replacement.
5. This one has been already requested I guess, but if you ever have opportunity for it, consider adding a possibility to select a number of voxels to create some sort of a "chunk" you can move, copy, paste or delete, sort of like you can do with tiles in FA2. Let there be a special tool that allows to "mark" voxels, and have a separate set of edit commands for these voxels (copy marked, paste marked, nudge marked, mirror marked). So it'd be possible to copy entire parts of the model: stuff like wheels, guns, lights, and so on without exporting layers into some image editor one by one then editing and adding them back.
How I see it working:
Step 1: Using a special tool you mark voxels to form a selection (Picture 1). The tool has an option to add or remove voxels from the selection and supports different brush sizes, also has an "unselect all" option. Marked (selected) voxels are visually different. The status of being or not being selected is not saved with the .vxl file.
Step 2: Using a special set of editing commands you copy or move (or delete) the selection, then position it as you need. Copied voxels do not replace the ones they are put over until a confirmation (Enter) key is pressed (step 3). Basically the clone is contained in a buffer until it's finally placed, so it doesn't consider each move a final one and thus doesn't automatically replace every voxel along its path as you move it, like it happens with SHP builer selection tool. Cloned voxels also look different, and they are always displayed over the voxels that actually exist (so it's like you move a layer). However if you press ctrl+c to copy a layer of the voxel, only the existing voxels will be copied, not the cloned ones (cloned voxels are only considered "real" after they are placed). The cloned selection is not saved with the .vxl file until it's placed (step 3)
Step 3: Place the copied voxels by pressing a confirmation key (Enter). After that the copied voxels replace the voxels which position they were occupying.