I think its innovative nature was part of the reason it's so widely misunderstood. These days, we have a bunch of book series focusing on characters other than the main cast, often with TV cast members appearing as guest stars. But at the time, there was nothing else like the Piper books; there'd never been a professional novel that approached ST from such a radically new perspective, a first-person narrative as told by a junior officer aboard the Enterprise. So the only thing there was to compare it to, the only thing that was even remotely similar, was the Mary Sue formula.
No offence, Christopher
, but the reason I think of Piper as a Mary Sue isn't because I'm at a loss to frame her narrative any other way, or because I can't tell the difference between a Mary Sue and a prominent "guest star." As a reader today, I'm familiar with plenty of ways to tell a Star Trek
story in prose, and I still believe she fits the "formula" (IMO) quite closely, unless you use the really narrow definition you came up with.
For one thing, I'm not sure why you insist a Mary Sue has to be a guest star, since even the original Mary Sue was the star of the fanfic story that originated the term. To use an outside example, Anita Blake is the star of her own book series
, and I would still describe her as a Mary Sue.
My own sense of a character's "Mary Sueness" doesn't depend on a character's abilities--or any trait that revolves entirely around how the character compares to other characters--but rather on the degree of the author's idealised self-insertion or general "self-indulgence," as mentioned earlier. (Basing a character on your own mother is certainly a step in that direction.) They can be written well or badly, but they're more common (and we tend to notice them more) in tie-in fiction because these elements often occur at the expense of the main characters
we expect to read/watch in action.
Granted, it was pretty common in early Trek Lit for authors to introduce impressive new female characters who took center stage -- Mandala Flynn from The Entropy Effect, Evan Wilson, Ael from My Enemy, My Ally, Anitra Lanter from Demons, etc.
Although sometimes, yes, the guest characters were outright Mary Sues. The classic examples IMHO are Elizabeth Schafer in Death's Angel and Sola Thane in Triangle, and Anitra Lanter fits the pattern pretty well too, though I found her to be better-written than the others.
The list you gave is a good example of how you need to give readers more credit for recognising this trope, since we can tell that some of those are Mary Sues and some of them are not. (For example, I would say that Evan Wilson and Sola Thane are Mary Sues, but Ael isn't.) Differences of opinion are more about matters of literary interpretation than about "misunderstanding" a work--like arguing whether a character qualifies as a tragic figure or not.