Would it not be better to use that in Acrobat? There is an Area tool in Acrobat, using separation it would be easy to view by colour. I can imagine that it would be possible to make a java script that does that... only i don't know enoug java.
In illustrator you can select objects with "same colour" and use the Artboard tool to set artboard to selection. There again I'm sure it isn't impossible to code a java script, but I don't have enough knowledge of code to write it.