Rescuing the Colour Underground from the Prison Zoo results in each of them grabbing a rope and climbing up to the blimp. Except you haven't rescued the blimp yet.
Maybe Pinky has a function that allows her the drop ropes from her arms so that the others can climb them?
Also, how in the HELL does jumping into a building and painting it in the first game transform it, of all things? Shouldn't it have exploded?
Why does Blob have a skeleton? He's a blob of paint!
The Hypno Ray is in geostationary orbit above Prisma City so it can catch the colour energy beams. How can it then "sweep the whole planet" with its hypno beam?
There's a question about the color-transmitting robots themselves. Why the hell does nobody investigate or try to damage them? It's not like they're hidden. They're on top of prominent landmarks, one of which is Prisma City's capital building. And all of them are beaming bright, concentrated columns of color that extend out to outer space. Comrade Black's master plan might've easily been stopped by somebody moderately observant and possessing a baseball bat.