Yes you can save mid-mission. Make sure you don't have anything selected and right click on the screen and you should get a dialog with an option at the bottom to save the game.
Also dont forget about the NWS fleet Command mod.
http://www.navalwarfare.org/ Naval Warfare Simulations make an all in one add-on that add tons of new units and weapons while giving them realistic loadouts and operation. You really have to have it, the game play is still the same, but its now much more realistic.