Ok, how the hell is Honor a Mary Sue? The author is a MAN. Genetic manipulation? Whoop-de-do. That's almost a given in the honorverse with colonists.
As for your contention that Piper is a Mary Sue, I just don't see it. She makes mistakes. She even is often so close to a problem that she can't see the solution for quite some time. A very human foible. So she McGuyvered her way past a computer sentry on her door in Dreadnought. And Kirk wouldn't have? Why does her emuation of her idol, Captain James T. Kirk, make her a Mary Sue character? Is it just because she's the unique creation of Diane Carey, who happens to also be a woman? The overarching theme for both books as I saw it, was that we were seeing a woman just as driven and resourceful as Captain Kirk, and also seeing what happens when Kirk has to deal with that woman regularly. Furthermore, we're not seeing that intelligence and resourcfuness without backstory. She doesn't suddenly become this die-hard character all at once.
In Dreadnought we watch her practically blow up the Kobayashi Maru simulator, not an uncommon feat for a cadet, but she was more creative than the average cadet in her method, using a trick taught to her by one of her friends using a communicator to tie in to the computer, forcing the simulator to fight itself. In Dreadnought, we get to see just how tricky shes always been courtesy of the flashback to the Outlast. This same flashback also shows her early raw potential as a commanding officer when she motivates Sarda to finally come up with a method of communication after he had been thinking, perfectly logically, in the wrong direction, wanting a sophisticated communications method when she just wanted any method that couldn't be read by the other teams, unlike the Jacob's Elementary Light Code one of those teams was using.
I find Piper to be a well thought out character with a good backstory, and flaws the same as anyone. A shame that she only appears in two books, save for offhand references in others (assorted comments about her being Fleet Admiral at some point, if I recall correctly).
I think Honor Harrington was also well thought out. She has her blind spots, like being unable to see that she is no longer the gangling youth she once was. I like her style, and that she never says die. That said, it would be nice if for once, Honor went up against someone better than she and she ended up winning by dumb luck instead of skill and trickery. It would make for a nice change of pace.
In closing, we REALLY don't have enough strong female leads in sci-fi on the whole. There is a bias, probably not consciously, toward male leading characters in the genre. This seems at least in part due to most sci-fi authors being male and not being comfortable writing a strong female lead or female characters in general. The female leads that do get written often seem to be just someone for the male to rescue and sail off among the stars with. I personally hope that I don't write that way. I try not to. The fairer sex is not at all the weaker and I don't ever want to write any of my female characters as simpering weaklings unless I have a damn good reason to write a female character specifically as such.
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