Thanks for the feedback! I will try and address each of your concerns one at a time.
Firstly concerning the storyline, while Palpatine, Dooku, and Anakin are all dead, there are many in the Republic that still push for war. In one of the early chapters of the fanfiction, Tarkin ends up replacing the Senator of Eridu and becomes the new head of the pro-war faction. Grievous finds that an implant given to him by Dooku had been increasing his aggression and limiting his rational thought. He has this removed, but he doesn't turn into a peace-loving hippie, he still wants to win the war.
There's a whole lot more to it than that, but if you want specifics I recommend reading the fanfic.
Next is your concerns about species. I had completely forgotten about the size adjustments to Damage Threshold, so thanks for pointing that out. I removed the Con bonus to Stenax and lowered the Viraanntesse's bonus to +2. I am a bit iffy about the suggested Natural Armor bonus, as I already gave the Stenax 3 different species traits. I am slightly confused by your critique about their flight speed
Maybe they don't use flight for "spiritual" reason but if it is something they can do then that speed should be listed
I have listed their fly speed as 8 squares, and mentioned their unwillingness to fly, could you be a little more specific? I also changed the Viraanntesse's stability bonus to +5, although I couldn't find any mention of an increased carrying capacity in the rules.
Slugthrower Training was included as early in the story a group of militiamen were shown to use slugthrower to shot "though" a lightsaber's blade (which only made the bullet super-heated). Both Hardened Resolve and Unflinching Resolve have had their Conditioning prerequisite changed to Shake It Off.
Finally, the Nonheroic Heroes sidebar is meant to represent b-list heroes that are important because the a-list heroes failed (thus creating the Infinity). I used 3 NH levels per H level as CL are calculated with the same method, though I have lowered the number to 2 NH after giving it another look.
Thanks again for the feedback! I will upload the revised version (build 0.02) as soon as I post this.