I may be missing something here, but most likely I’m not. Here’s the suggestion:
How about adding ability to save “workspaces”, i.e. all opened projects not necessarily connected via layers. You already got the code, you save what I mean by workspace on exit and offer to reopen on startup, all that’s really needed is to add ability to save it to a file and reopen from a file. This would allow for saving thematically connected sets of projects (e.g. graphics for your game) and open them on a whim, which is especially important if your work on multiple projects at once.