First, the Gedcom standard is very loose and has many interpretations, from their infamous ANSEL character encoding, to the CONC and CONT tags, to the NAME tag which uses the forward slash (/) to split the first name, last name, middle name, name prefix and name suffix.  The Gedcom documentation provides no meaningful examples for the NAME tag. I wrote several time to the Gedcom "support" and never got a single reply.  As a result, different applications interpret the the NAME tag differently, resulting in data distortion.  To "fix" their problem, the Gedcom committee came out with Gedcom 6.0 which uses XML.  I was not able to find a single genealogy application supporting Gedcom XML.  My guess is the Gedcom 6.0 specifications will never be used by the genealogy community.

Second, there is a wide variety of genealogy applications, having GenoPro at one end of the spectrum.  GenoPro is graphical application requiring additional drawing information such as the layout position (x,y) of each object.  Exporting to Gedcom is fine, however other genealogy applications care little about the family tree layout.  As a result, the genealogy application may not write the x,y position back into the Gedcom file, and next time you import your Gedcom file with GenoPro, you will loose your family tree layout.

GenoPro uses GenoMaps and hyperlinks, a unique feature seen nowhere in other genealogy applications.  Well, each hyperlink causes a lot of trouble because it creates duplicate individuals within the family tree.  Other genealogy applications importing the Gedcom file are likely to create two individuals rather than linking them. See An explanation of how hyperlinked users on different genomaps are exported in Gedcom format for details about this issue.

In Gedcom, a place is a text field while it is an object in GenoPro.  As a result, GenoPro can store additional information to a place, such as multiple pictures and much more.  Well, this data can be exported to Gedcom, however other genealogy applications are likely to miss all those places because they won't recognize the tag.  The same can be said for twins, labels, bookmarks and more.

Finally, there is the issue of upgrading the import module to use a new parser.  You are welcome to read Gedcom compatibility with genesreunited for details on this.