Janeway is in half of Full Circle, but, if sentiment(s) expressed in another thread related to the topic (in the Voyager forum) is any indication, there's a section of the Voyager fandom that are diametrically opposed to the Voyager 'relaunch' fiction because, in order to conform with Nemesis, it changed the status quo of Voyager and relegated Janeway to a supporting role for the period of time between the start of said fiction and her death.
I expressed this in the other thread, but I really don't understand this whole 'Voyager isn't Voyager without Janeway' sentiment, because it's complely anamalous and organic to the Voyager fandom (I haven't come across a single fan of DS9 - the first series to go forward in literary form without its on-screen captain/commanding officer - who is opposed to the DS9 post-finale fiction because it doesn't include Sisko), and haven't yet been given any form of explanation for why the sentiment exists.
Well, I'll try. Sisko was "disappeared" from DS9 in canon. Even so, Sisko was eventually restored to the novels. I suppose it was a necessity for the DS9 fans to accept that Sisko was absent for awhile (I'm not saying he was dead), and yet the editors/writers eventually restored him. Sisko's "death" in the finale was also respectful and even heroic, and, more importantly, it was the end of a long arc for him as the emissary. It was part of who he was and totally in character.
By contrast, Janeway was "killed" in the novels, and actually in a TNG novel, and was totally out of character as she "died" (yes, I have read portions of PD's novel). She was unrecognizable to me as the Janeway I'd watched for seven years on the screen, and I felt that the way she was treated was wrong for the captain and main character of the Voyager series. Add to that the paucity of Voyager novels over the years, and you might understand that I want to continue to read about her exploits because I like her and find her to be an essential element to Voyager.
Now, I'm not sure what you mean when you say that you don't understand "this whole 'Voyager isn't Voyager without Janeway' sentiment, because it's complely anamalous and organic to the Voyager fandom." How is that so? There was a terrible outcry when Spock died in the movies, so much so that he was immediately restored. Sisko was missed by the fans and returned to the novels. Trip was missed and almost immediately restored to the novels. Data has been restored to the comic books through B4. I don't understand what you mean by "anamalous and organic." Maybe you could explain that to me?
Finally, I think with Janeway's "death" there is an element of "gotcha" on the part of some fans that is very unseemly. They don't like Janeway and they enjoy turning the knife in the sides of the fans who do. To me, that's just unfair. No one gloated when Jadzia or Tasha died--"haha, she's dead, live with it." No one was happy when Sisko "died" or Data was destroyed. Everyone mourned Spock's death. Perhaps you can explain this "gotcha" reaction as well?
I haven't read any of the DS9 novels set after Unity (the novel in which Sisko returns from the Wormhole), but, based on that novel and Sisko's role in it, I would be extremely surprised if he was anything other than a supporting/tertiary character (which is the exact same role that Janeway plays during the portions of Full Circle in which she appears and which are set prior to her death).
Regarding my statement concerning my lack of understanding about why there's a section of the Voyager fandom that feels that Janeway must be present in order for Voyager stories to actually be Voyager stories, I don't know how I can explain it any clearer or more succintly than I did in that other thread, but I'll reiterate my point here. DS9 fans lost their captain as well, and yet, as noted in the other thread, I have not come across a single fan of that season who feels the way that you and others do about Voyager and Janeway (i.e. 'DS9 isn't DS9 without Sisko'), both prior to and after his return in Unity.
I am an admitted Janeway fan, and recognize that she became very central to Voyager's storytelling; however, as I stated in that other thread, I never saw her as being the 'be all/end all' of that series, nor do I see her that way now.
I'm going to leave out discussing the exact situation in which Janeway was KIA and whether or not it was mishandled, due to the fact that I haven't yet had the opportunity to read Before Dishonor and come to a conclusion myself regarding how Peter David handled her death, but I do think that there's a very fine line between objecting to something and and coming out so strongly against said thing that you become obsessive, which is the feeling I have gotten from comments you and others have made with regards to Janeway's removal from her centralized role in the Voyager fiction, and her eventual death as chronicled in Before Dishorn (which, as noted in the other thread, I see as two separate issues).
I'm not going to comment on whether or not there's a 'gotcha' reaction on the part of some Trek fans (Voyager or otherwise) with regards to Janeway's death, but would like to say that maybe you and others who feel passionately about Janeway being involved in anything relating to Voyager ought to take a look at the possibility of the fervor with which you exprss your opinion(s) having given rise to such a reaction from those who do not share that opinion(s).
Finally, I'd like to address your point concerning the difference between Sisko's removal from his central role in the DS9 narrative and Janeway's removal from her central role in the Voyager narrative:
The fact that Janeway was KIA in the novels -which are non-canon - makes this idea that 'Voyager isn't Voyager without Janeway' even more baffling to me, because I see a very obvious solution to it: if you want Voyager with Janeway, just go watch the canon and ignore the novels. The editors and writers of the post-finale Voyager fiction have tried to make the series' narrative evolve, and have chosen to do so without Janeway occupying a centralized role (although that is something that wasn't entirely in their control, given that the canon of Star Trek Nemesis made her an Admiral and gave her a desk job). The fact that she was KIA ultimately has no effect on that decision, as it was made prior to her death in Before Dishonor, which is indicated by the fact that she is very much a supporting character in those portions of Full Circle in which she appears and which are chronologically set prior to her death.