Since Flotilla ends pretty quick anyway, I don't get too miffed at the lack of a save. The whole point is to restart the game constantly and see what new weird things you can run in to. On the other hand, I would enjoy a longer or an endless mode.
In case you're running into the problems everyone seems to have with it feeling unplayable and way too difficult, remember to explore the options for setting your ship's rotation and facing. If you just tell them to move to a point, they will probably end up with their weak spot pointing towards the enemy, and die. You have to make them rotate around their various axes in order to face your strong areas towards where you think the enemy will end up.