I think it's primarily personal preference of features and how things are stored and presented. While Wallabag is more a Pocket/Read It Later alternative, LinkAce does not save the website itself, but a reference to it including the taxonomy you assign to it. It is intended to be a long-term bookmark archive, but without handling all the website archiving on its own.
Just a heads-up. Found that a while ago and much prefer it over wallabag.