The Battlecruiser's ability takes energy, whereas the Thor's ground to air attack is standard. The Battlecruiser's ability is to make it more effective against what it is already effective against. Also, users have the choice to go with the air to air missiles or with the Yamato Cannon.
If you are in a game where they have massed a lot of light air units, then you know what to get. This ability simply gives the Terran player more flexibility of options against air in late game. Smurfz: " Karune, if your reading this... more.
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