This isn’t the most important thing in the world, but I’ll throw it out there.
In addition to auto-save, could we have a manual save option? It could potentially be helpful in a particularly difficult challenge or player puzzle, where you want to try a number of different things but don’t want to loose any, or in a lab where you don’t want to share a solution quite yet, but want to make sure it’s saved, or if you want to work on something across computers. I know you can do it with copy and pasting sequences, but at some point it would be nice to have this integrated into the game.