The things that bother me most about c2 are small things, like not being able to set size of layers width and height separately, or not being able to rotate tilemaps with their collisions also, or things not having expressions for properties you can set elsewhere. Also shader support is lacking- you can't make shaders that use multiple textures for reading/writing data, for example.
Also, there could be a lot of area for improvement in ways of organizing your eventsheets/events to be more readable, like color-coding groups. Also tracking where undo/redos are made would be useful. A way to see where functions are being called- basically ways to help see the flow better so you can jump between eventsheets and not get lost.
Also, families could be improved- It is often annoying if you have a variable in one family and need it in another, and have to rename the first one and then add it in the other, then go into the eventsheet and change which events use the old variable to the new one.
Sprite animation system could be improved- spritesheets for example, tiled sprites, etc.
Also, would like to see more support for in-game menu systems, as that is a very important aspect of games that engines overlook.
Also it is annoying with the export problems, yes, but I believe that will improve.