Enterprise Guide projects are actually zipped files. If you rename your myfile.egp file to myfile.zip, you'll be able to uncompress it. Take a look at what you get: it is a set of xml, sas code, .... You could perhaeps base your comparisons on this. But it won't be easy for sure. I don't think there are other ways to compare egp files.
I don't think it is possible to merge or import process flows from other project files.
I hope you'll get other inputs. It is an interesting question !