Here is an interesting thread from the The Master Genealogist mailing list on RootsWeb.
The technical as well as the philosophical aspects are considered by the members of the list when handling the newest major information source for genealogists of all stripes.
In The Master Genealogist, version 8 (TMG8), the user is forced to choose between using end notes or footnotes. The differences between the two are remarkable and have an enduring effect on the reader and researcher.
Elizabeth Shown Mills and others have written on the subject and I’d like to add to and paraphrase some of those writings here.
Footnotes are the recommended style in genealogy
A casual reader may not be interested in the source material and can safely continue reading past the end of the page with footnotes. A researcher, however, needs to have the footnotes on the same page.
Benefits and Problems with Footnotes
The major benefit of footnotes is that they are on the same page as the statements to which they relate.
The major drawback of footnotes is that they can be lengthy and contain information not directly relevant to the statement. The best way to handle this latter is to find a way to merge digressing information into the text and add a citation to it.
In TMG8 the problem is compounded by the use of “ibid.” The forced use of this archaic and often confusing Latin abbreviation can lead researchers to cite the wrong source in their own work. It can also cause readers to misunderstand or misread a critical source citation.
Benefits and Problems with Endnotes
The benefit of endnotes is for the casual reader who is not so much interested in the sources as she is in the content about those sources. This type of reader may become a casual researcher and look up a source statement, but is generally put off by having to flip through numerous other notes on the way to finding the one she wants. This effort can lead to problems in finding and thus correctly interpreting the information in the endnote.
TMG8 handles the ibid problem differently with endnotes. You can combine consecutive notes and have them all together as proper. The problem with TMG’s output of endnotes is that they are “uniqued” and not consecutively numbered in the text. Thus you get note 20 followed by note 8, and then note 34. This is meaningless to a skilled researcher and can throw them into a wasteful loop of figuring out which notes are which.
The final grain that tips the balance against using endnotes in TMG is that they are not connected to the text as is proper. They follow the text as additional paragraphs, so you can’t click on the note number in the text and jump to the text of the note later in the document. You need to flip so many pages to get where you are going and maybe lose your original starting point because of the non-continuity of the numbering mentioned above.