I can get you on something there! Kirara can indeed survive in an oxygen-poor environment. In the series, one of the later Alliance attacks on X-Bomber succeeds in damaging the oxygen production plant. Lamia has just started becoming F-01 in earnest, so is able to breath in the thin air. Kirara is still up and around at this point, and helps Lamia by getting the crew to sick bay. Genesis does start a few months after the end of Star Fleet, so funerals, services etc would already have happened. Another thing to remember is that it would be incredibly difficult to locate and retrieve Kirara's body in space - and so there's nothing to say it was ever found. Also note that the entire Skull, along with whatever crew were still alive, vanished as part of the F-01 birth. So I don't think it's stretching things too far for Kirara to have been caught up in that. As for a planet of Kiraras - urm, there wouldn't be a lot of conversation!
I suppose I could have fleshed out the reason for Shiro's choice further, but then you start getting into a lot of explanatory blurb which you're supposed to avoid. As it is, it's up to the reader to attribute their own motivations like the ones you've suggested. As for using an Alliance member - they wouldn't necessarily be less problematic. Bear in mind the civil war that was brewing. Would an Alliance officer, hungry for power, want the Imperial Master back on the scene? Also, remember that F-01 is partly responsible for X-Bomber being lured into the Heir's trap and the Heir could predict that happening. So at one fell swoop you remove a hero of the EDF, and also capture the one ship they had that could stand up to the Imperial fleet, whilst bringing your leader back. Nice and neat, if a little over complicated!The idea of a female second in command is interesting. There's also a question mark over Shiro's mother in a sense - with his father (or so we believe) involved with EDF at a high level, it makes you wonder if his mother is also around playing a significant role. Had I approached Genesis as a sort of out and out novel there'd probably have been more secondary characters which would have given scope for more female characters, but it was quite a time intensive process to write as much as I did! You might like to read some of my other fiction which does include female characters:http://www.adamantium.demon.co.uk/fiction/As
for Revenge of Makara, that's up to Shane - I think he may be intending to launch it in a couple of weeks, the 20th anniversary of the show's first showing over here...Edit - or then again, as Shane just posted while I was writing this, it could be out this Sunday! And me X-Fighters are in it, niiiice
Ain't continuity grand!