One of the big things I miss from Total Annihilation, was the game modes. There was Sudden Death, where if your commander died everything went pop and you respawned somewhere, so you get to do all those scenarios where the opponent has a full base and you're laying a fresh siege. And more importantly, the normal one where you kept going even when your commander died. If he DID die you lose a massive amount of storage and a nuke goes off in your base, but you could also use him as a cloaked nuke to walk into the enemy base so they cant anti nuke him, right before sending in an army led by Krogoths or Bulldogs.
You got things kinda backwards. Assassination was the standard mode, the game was designed around it. Annihilation was the secondary non-standard mode. Mike