Here are some tips for using GED-GEN more effectively.
If you exclude living individuals, they will not appear on any family page. This may make some family pages unreachable from any other family page. However every family page generated will be reachable from an index page.
For example if the parents of a deceased child are living, and you exclude living individuals, the deceased child will appear on a family page without its parents listed. This creates a "gap" in the flow of your family pages for someone following the parental or spousal links. Such a page would only be reachable through the child's name in the index.
A similar situation occurs if your GEDCOM file contains individuals that are not associated with a parental or spousal family. GED-GEN generates a family page for the individual, but it will contain no links to other family pages. Such a page is accessible only via the index.
After you use GED-GEN to generate your family pages, you may wish to include HTML links to these pages within other web pages on your website. For instance if you have a biographical web page for an ancestor, you might have a link to their corresponding family page.
Keep in mind that if you update your family data, re-export a GEDCOM file, and re-run GED-GEN, the files generated may have different names. If you add or remove families, or change which individuals are exported, your genealogy program might number the families differently. GED-GEN uses these family numbers to create unique web page file names.
See the discussion about Family Page References for more details. Always test the links in your other web pages to verify they link correctly to your GED-GEN-generated files.
If you want more control over what is generated for individuals in your GEDCOM file, use your favorite genealogy program to export only the desired individuals and/or information about them. Or, use any of the widely available programs that change a GEDCOM file by filtering such information.
For instance you could use your genealogy program to create a report listing only living individuals. You could then export the individuals in that report to a GEDCOM file and then run GED-GEN.