A checkpoint system would have the same problem: when you hit the checkpoint, all objects and their relations need to be captured. You can't defer creating such a checkpoint until it's more convenient. That is, no fancy complicated things like active Lightning Storms, no units sparking, no units having any AttachEffect, and so on. Such a game situation is atypical. After the mission starts, entropy increases. It only goes down if you approach the end and all units and structures are destroyed, but it will never become zero again.
Also, you can't reasonably detect a good time for such a checkpoint. If the game would check every frame whether it is safe to save, then, whenever you would try to save a game (or auto-save is triggered), the game would just start to lag badly until the end of the game, because it takes that long to find out, and it just won't happen anyhow.
It's not like I haven't thought about all this for years, and there has been hidden progress, though kinda not during the last two years. I know what's missing, but the problem is the motivation: for whom, and why? It's the same thing that stopped me working on Ares two years ago, and the same thing that put me on hiatus for the last six months. Only few people care, so why invest time?
Good examples in C&C where even WW (mind: with access to the source code) messed up:
- In TD, when Nod fires a nuke at you, save and load. It won't impact then.
- Saving and loading restores the initial Tiberium and ore on the map, and even resets it to grow again.
- Crates aren't saved, which can be surprising in campaign missions, if the crates are important.
Created my acount just for you. When I saw your website with all of the bugs and features in the backlog a few months ago I remember thinking "This is a HUGE undertaking. What a boss" "https://bugs.launchpad.net/ares" Because I know how hard developing and extending this game is. See this discontinued mod for example: "http://www.moddb.com/mods/red-alert-3-paradox" they had huge plans and were busy for years but they ultimately gave up "because the engine worked against them every step of the way."
You managed to work with the engine anyway. You actually punched it into submission at this point. Huge respect for that.
Set up a patreon and I'll give you something every month just like solais. Many other will to I think if you make sure you have some exposure.
And then on the savegame thing. You say you need to go and check if any states will recover correctly. Well... add it in there (which will be a feat in itself!) and don't extensively test it. It doesn't have to be perfect at all. Just enough to make a game playable after a save.
I appreciate all that you have done!