Tying stat increases somewhat to Promotion might be a bad idea, considering.
I think that nuXcom-like abilities would have to be done in more subtle ways. NuXcom is too arcadey and table-top ish, while UFO Defense is more simulationist.
We already have the help with Morale that officers give.
I think perks and abilities would have to be more subtle, things tied to ability to command, lead and inspire example. Say, make a unit stop panicking, execute mind-controlled unit for X turns of no M.C, Imperial Guard style, +x% reaction chance, small increase on carry weight ("wimp soldiers? Not in my fireteam, soldier! You WILL carry that Rocket Launcher and four large rockets!"), etc.