+2 Morale is probably what I'd rate the lowest of these three. Extra morale isn't bad by any means, but it's going to be a minimal effect in the early game and it's completely fallen off by the mid to late game, when enemies are so plentiful, everybody will be hitting 150 routinely before stage's end.
I went with the +2 Morale for my first run and found it pretty useful in the early to mid stages, it helps getting to the requirements for strong/map attacks a bit quicker. And I didn't really use much Spirits or needed that much EN early on.
But you're right, past the mid-game the effect is starting to feel less and less noticeable. There's usually plenty of grunts to kill right from the start, and easier ways to quickly increase Morale when needed, between self-buffs for pilots, Extra Commands, ect. For my next run (or if I could re-pick), I'll probably got with the +3 SP per turn. It's not even for the Fortune part as I don't really grind cash and tend to forget the skill even exists, but I'm relying a lot on the 100% Hit/Evade skills against bosses, and SP can drain quite fast when there are several, so an extra cast here and there could be useful.