Having the two cockpit modes (combat and analysis) allows you to use certain tools and stops you from using others (eg. you can't use the wake scanner or interdictor while in analysis mode). You also have another key to toggle between the two modes. At the very least the main difference is the appearance of analysis overlays on planets you've surfaced scanned. This doesn't make sense. It would be better to do away with the two modes limiting the SC tools and just have a button to toggle on/off the overlays - just like toggling on/off the night vision.