In fanfiction, "alternate universe" refers to a story that takes the recognizable characters from the fandom and puts them into a completely different setting. Austenesque authors lean heavily toward sequels and variations, but there are a few alternate universe stories out there.
In Pemberley Ranch by Jack Caldwell, Jane Austen goes to post-Civil War Texas. Beth Bennet is a Yankee with a passionate hatred toward former Confederate soldiers and slave owners. Rancher Will Darcy is both--or so she assumes. Meanwhile, Will is too proud to reveal the parts of his past that might make him more appealing to the young lady.
Obviously, when you take a Regency story and move it across the Atlantic 60 years later, there are going to be some changes, and some things won't necessary translate well. The key to an alternate universe is digging deep to find out who your characters actually are, and then deciding how to portray that in your new setting.
Confused? I'll give an example. In Pride and Prejudice, Darcy and Fitzwilliam are cousins, almost as close as brothers. They share the task of caring for Georgiana and it doesn't take much reading between the lines to say they trust each other implicitly. In Pemberley Ranch, Fitzwilliam is Darcy's foreman. The same level of trust exists between the two men, and thus Fitzwilliam plays much the same role as he does in Pride and Prejudice--he's just wearing a different hat.
That kind of finessing takes work. You can't just throw all the characters up in the air and hope they fall into place; you really have to think about who they are and how they relate to each other. That level of dedication is what makes a good alternate universe stand out from the crowd.