Maybe a good solution would be a Hold Position command for squads. They'd stay in place (e.g. right in front of missile units) but fight those who come within melee range. They'd not move unless routed, or possibly beserked, but instead would maintain a defensive wall in front of vulnerable troops.
For me, that'd close the biggest tactical gap. You can Hold and Attack, but nobody can stay back and guard, unless they are Guarding Commander.
It'd also be nice, as has been previously mentioned, if troops ordered to flee (as opposed to those who broke) would stay with the army after victory.
Aside from that, formations would be a great and powerful addition, but additions are very different than things that feel "missing" when not there.
Maybe instead of true formations, the ability to have the troops line up in other than simple boxes? That wouldn't need to have any change for the battlefield aside from different start-up positions, and I wouldn't think it'd be too hard to add AI capacity to know when a line (for defensive men) is better than a box (for massed troops).
All just my 2¢, of course.
Re: suggestion about commanders
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