Here are a few items:
- You cannot scroll over empty space. If you use empty space inside a map as a border or decoration it can make scrolling around your map a chore unless you zoom way out.
- Some entities don't remember their settings. For example, accumulators cannot be set to output anything other than A if they are wired to a circuit network. Lamps do not save 'Use Colors'. Requester chests do not save any values. I'm sure there are more that I have yet to run across (edit: like disabling output on constant combinators.)
- Technologies cannot be set to researched without adding a lua script. This has been mentioned on the forums.
- Something else that has been mentioned is a copy/paste function, which would be great if it worked like blueprints, i.e., deselection of entities, allow option to include/exclude tiles and/or entities.
- The primary and secondary buttons don't function the same way for land, resources, wires and entities. Place land, wires and resources with the secondary button. Place entities with the primary button.
- Allow higher speed and intensity when placing resources (coal/iron/etc.) If I want several million units of a particular resource placed on the map it can take a while to place, long enough that I have a short autohotkey script built that holds the mouse button down for me.