Not really. We are under no delusion that a complete phylogenetic tree will ever be mapped, there’s just too many species across too much time, and astronomically low chances of preservation, not to mention large stretches all over the tree where body plans simply aren’t preservable. It’s indeed an often misused term, but it’s a useful one in the right context, where you have a distinct intermediary (Darwin in fact used the term “intermediary links”, not “‘missing”) whose ancestors and descendants share morphology you can place on a continuum, with the intermediary somewhere in between.