Thanks for your post! Since this is the first pass integration with Fusion a number of things that were classically Eagle have been shuffled around or are in the pipeline, as we rationalize the alignment with Fusion. I'll take each one by one:
1) Assignable keys to commands [Options/Assign...]
This is in the pipeline but not there as of yet. You can still run these from the CLI but we are working at implementing Fusion's command framework to bind to commands in the Electronics Workspace in a somewhat cleaner, more consistent way.
2) Set Colors etc from Settings menu [Options/Set/Colours etc]
Color options are located under the preferences located by clicking on your username in the upper right corner or from the Display command in the main workspace. DefaultColors.scr will also work to restore eagle colors.
3) Set User Interface
UI options are also located under preferences.
4) My .scr for my own custom buttons/functions no longer works
This is something we are discussing now. We are planning to support the key bindings to CLI commands (SET, etc) but again, this is not in the current implementation and will take a somewhat different turn to ensure we have the best of Fusion and what you experienced with SCR files avail. SCRs to define keyboard shortcuts and UI layout will not be a part of that but the general workflow will accommodate equivalent customization.
5) A way to reduce size of menu/function icons
You can so this thru the OS using the compatibility settings for the Fusion360.exe and targeting just the app. What OS are you running?
Best regards,
Matt Berggren
Autodesk