I had exactly same thoughts today!
Multiple groups are a must. I was thinking about fixed number, six groups, and you can assign on a party screen which troop type goes to what group (add a number next to troop name, clicking on a number would change it).
I was also thinking about merging it with a battle morale, so you could route specific group. This way cavalry charge would have a meaning and impact - you deal a massive damage in a short period of time, defenders breaks and retreats. Now there isn't much advantage to this maneuver, cavalry is surrounded and slaughtered.
As for heroes commanding groups - I made one hero an infantry man, another an archer, dressed them in a nice blue armor, and voila, it seemed as if they were officers. Very nice, you should try too.
With this relatively simply additions M&B would gain a tremendous amount of tactical depth. Flanking, keeping some troops in reserve, timing charges - all of that would matter. As The Wandering Knight said, breaking enemy formation would be essential. This way enemies would arrive to your formation one by one, easy to overwhelm and defeat. I think you wouldn't need a formation like line or wedge, as keeping close to each other is big enough advantage in M&B.
Battle morale is already implemented in mods, hopefully advanced grouping will be also (as it is in development right now), so one day we should have all of this.