I wonder if you could also make rotational play more interesting. Maybe you get X% EXP in combat and then you get a similar X% bonus when training back at base. I guess the idea here being that you learn lessons in battle and then when you return to training, you train the things which you think will best improve your ability to win fights against aliens.
This would make battle - rest - battle more powerful / optimal without the stick that is the stress system...
Just some more thoughts :).