One of the main reasons for Starcraft's "Masterpiece" status is the fact that all three races were absolutely different in terms of gameplay and behavior, and aside of resources, have little in common.
Different technological development styles, completely different building management and unit production, and aside of minimal parallelism, there wasn't much in common in terms of unit behavior.

Now, the mothership, is clearly a very special unit, which causes great balance concerns.
But from my experience, I am 90% sure that niether Zerg nor Terran will get a similar unit, due to the simple fact, that it doesn't need balancing via another mega-unit. Just like the Terran Nukes never needed balancing via some mega-spell - the mechanics of the game took care of that.

So what do you think - What will happen to the Protoss Mothership ?

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Admiral Anderson Mccutcheon
Inspector General
TerranoZergus Project