Actually, standard conquest-style maps work better in vanilla because of the Commander.  The entire map doesn't always need as much funnelling structure/stricture if there's someone looking at the "big picture" and telling different squads to stay put.  With a good Commander, he can scan the map, see where the enemy is going and tell Squad Leaders to defend, attack, split up, etc. as needed.

The main reason things become "like whack-a-mole" is because nobody wants to be left out of the action. A competent Commander (not one who goes flying around the map on his own) will find use for each Squad.  Even defenders will stay where he tells 'em to be because he knows there's an enemy assault on the way.

I've done very little Commanding in vanilla, because I really hate the pressure.   Because of that, I'd spawn in the uncappable base, and stay there the whole time, trying to give everybody a useful order.  The only reason I'd leave is if I noted a single enemy dropping in behind our lines, and knew I could stop him myself faster than ordering a squad back.

If we could find more "Star Warsy" abilities for the Commander, and could somehow limit him to staying in one place (lock him in a (static) shuttle for attackers, in a command base for defenders), that'd really improve the teamwork, and open up the possibilities for more Conquest maps.