Allow the user to re-arrange colors in the Styles menu.
"Bake" a layer so all its numbers go to zero. That way, if you import it into another project, it won't do anything unexpected (like translating across the screen).
Nudge all keyframes to the right and left of the time slider, using (,) and (.).
Create different colors for the layers (more bright and colorful than the ones at present, which I sometimes fail to notice).
Lock a layer so that the art cannot be changed.
Allow a switch layer to be bound to a bone even though the vector layers inside the switch layer may use bind points. (This would be helpful, as my latest switch layer has 40 hands and I can't bind it to a hand bone.)
A new, more convenient way to access switch layers, so you don’t have to use the Layers window. Maybe there could be two or three switch layer buttons in the workspace, and the user could assign specific switch layers to them? And the user could also choose an icon for the button, like a mouth icon for the switch layer with mouths?
When you create a new Styles color, make it appear as the default color (Style 1). That way, if I immediately make a shape, it will be the new color.
Make it so that you can set Smart Bone Action defaults. For example, I would set it so that a keyframe will appear on frames 1 and 96 and one on the midway point, frame 48.
Make masks easier to use by including some helpful text to remind you what all the choices do, and the correct order of layers.
Make it possible to copy two things at once: a smart bone action and a single layer. That way you can duplicate an arm or a leg and keep the associated SBA. Also, automatically rename the copies by adding “copy” to the names. Or automatically change "R" to "L" or "Right" to "Left."
Put a “reset bone” button on the workspace so I don’t have to use the menu. (This seems like a common thing when animating, but maybe it's just me.)
Oftentimes when I create a new shape on a layer with multiple shapes, the arrow keys won’t lower the shape until I exit the shape and re-select it. The newly created shape is selected; I see the checkerboard pattern. I feel like it should be able to be lowered by the arrow keys.
“Document Markers” seem to take up more space on the timeline than they need. They take up as much space as three rows of keyframes.
Create a way to 100% isolate Bone Strength. For example, presently if a puppet raises his arm, points in his neck move a little. What if you could draw a “force field” between the arm and neck, so that bone strength stopped at the force field?
I sometimes have bones that overlap exactly, which makes it hard to select the correct bone. Invent a quick way to select the desired bone when multiple bones are stacked. Maybe a menu choice called wiggle bones? It could move every bone a few random degrees, making it easier to grab the desired bone. A wiggled bone will not effect any artwork, of course, and would return to normal once a bone was selected.
Set the default “cycle” to frame 2 instead of 1, since that’s the one used most often, or allow the default to be changed.
Have a tip of the day. Like, every time you open Moho, you get a tip. “Did you know that you can...?” Include a link to the page of the Manual with more information, or to an online tutorial. Also, you can click a button and get a new tip.
When I select a bone and use End Flip or Side Flip, the bone rarely does what I want. I guess I want a button that will Mirror the bone? If a bone is pointing downward slightly to the left (7 o’clock), for example, I want it to point downward slightly to the right (5 o’clock).
Group the Styles colors into folders based on characters, folders that can be closed and expanded. This will make the menu tidier when you have a ton of colors.
If you like the random rag doll physics of a particular object-impact on a character, save that exact animation so that it repeats. Some rag doll physics I like more than others, but they change every time.
Make it so that you don't need Bone Strength to use rag doll physics. Maybe just give bones a default Bone Strength for the impact only?
Color adjustment in a Layer Setting (or wherever). Sometimes I want everything to look more blue because it's night, or more yellow because it's hot. Something quick and fast that doesn't involve masks. Maybe a Color Adjustment Layer that only affects all layers below it in the Layers window?
That's it!

Moho is an awesome program. Keep up the excellent work, Lost Marble!