mother ship does have weaknesses, it looked uber strong in the demo because they kept recharging the shield everytime it casted a spell (I think every time it casts its spells, its shield goes to zero)
No, there were 3 meters on the HUD for the Mothership: Energy, HP, and Shields. The reason the shields kept going down when the spells were cast is because it opens up the mothership to attack and the shields were getting pounded by enemy forces.
Also, if you notice the animation, the shield on the top of the Mothership goes down whenever it does its Planet Cracker, and the narrator says "normally this would open your Mothership up to enemy attack." I think that when the Planet Cracker is in effect devastating ground forces, anything in the air can get past her shields and do direct damage to her HP.
Not sure if this applies similarly to Black Hole, where it only affects air units and probably exposes you to significant damage from ground units.
Also one thing I noticed was that when you activate Time Bomb, the missiles passing through it don't stop until they get close to the center. As long as whatever's being protected by the Time Bomb stays in the center, it's safe from those missiles, but the instant the Mothership moved through the bubble to approach another of the Missile Turrets, it started getting hit by the extremely slowed missiles that were just managing to get through the field to her.
Each of the abilities has a weakness to it, and the Mothership itself may be tough...but you'd expect that of a ship that you can only have one of, and that costs so damn much. If the Mothership was too weak and easily dealt with, it'd be a pointless unit because nobody would bother to spend the resources to get it out.