I think the way it is now is fine tbh.
In Mirrors Edge/Tomb Raider style game, there are several hard bits per level - the levels themselves are split up into a series of miniature levels and usually a checkpoint.
Classically WC games are/were split into groups of missions within a system and it depends on how you do in all the missions to how the system turns out, so in effect there is little difference.
My issue with Mirror's edge isn't the checkpoints exactly, though some of the later ones are pretty punishing especially if you are trying to not shoot anyone. The biggest complaint is that you ***cannot save at all*** until the end of the level. If you quit, you don't restart at the checkpoint next time you play, you have to replay all the points in the level until you get to the next level. That's not so bad early on. However, when you barely make it through by the skin of your teeth, only to find the next section just as tough, it becomes a chore when you must turn it off because you need to sleep or it's time for work or something.
This is more like having to actually play every mission in a given system in a WC game (3 to five missions ) before being able to save. If you turn off the game you have to replay them all instead of just the last one that you are having trouble with.
I don't personally have a problem replaying individual WC missions ( I do remember some of the tough ones taking 30 - 45 minutes back in the day) but I can see where some people might want at least the option of mid mission saves on some of the longer missions. I don't know if the Duke3D system would be necessary but it's an interesting option. In the classic WC games you only ever really had a lot of trouble at one or two nav points anyway, so letting the player save after he clears a nav point and autopilots wouldn't be making it so much easier as less tedious. And they're limited to their ship's/missions's state at that giving time of saving as opposed to given a fresh ship.
One thing that peeves me at times though is having to sit through a really long cutscene, perhaps in the middle of a mission and then not being able to skip it if you have to replay the mission. It may be a cool cutscene, but by the 3rd and fourth time it gets annoying, so they either need to let you skip it or autosave your mission as soon as the scene is over.
I'd have to give coop some thought, thought, though I like the idea of having multiple wings with different objectives. WC4 has something like this though it wasn't fleshed out much beyond comm chatter. The developers did tout the new features as being special with the world living beyond your own mission. A quick example is catscratch's satellite recovery mission, where you have to abandon your own objectives to save him, though there are also secondary mission assignments listed in the computer for hawk and other on many of the speradon missions among others...
Theoretically, the wings were supposed to be litterally doing their missions while you did yours with potentially you being able to find the other wing and watch them going about their objectives, whereas practiaclly I'm not so sure the game ever actually acheived this, though I remember doing badly on the capture the carrier mission once and another wing coming to assist me... maybe I imagined that though.
A similar system could be used for coop, but I think their objectives would definitely need to intersect to make it worthwhile. On pair sweeps ahead and clears out navpoints for a the pair in a bombers or something... or a two point ambush with one pair attacking a carrier group from opposite sides where it's essential that it be coordinated so that you attack at the same time, or one wing is a diversion to draw the enemy fighters away from the actual target... I'm sure you can think of more creative examples.
I don't really see saving in Coop being that different than in single player though. whoever hosts would have all the relevant save info on his PC Or console, with multiple save slots you can go back to whicheveer mission you saved at. But while you are playing the mission, might be nice if there was a way in coop to at least save at certain navpoints ore something like that.