What I think needs to be added to the factory is..... a secondary mode for the Thor. Think of it from a design perspective. Currently every unit apart from the Thor that pops out of the factory has two modes:
Hellion - normal mode and battle mode
Tank - normal mode and siege mode
Widow Mine - burrowed and unburrowed
Yet the poor Thor is stuck in one mode only firing his big-ass cannons. What I suggest is that the Thor lose his energy and the strike cannons, instead gaining another form called "Mobile Thor" where he transforms into something looking like a very very big Hellion. In this mode he can move faster and shoot small numerous missiles which can help quickly take down Mutas and Immortal shields, thus plugging the hole in the Mech arsenal.
And it would be better from a design standpoint since then all Factory units would be able to "transform".