Still, do you think a 'Command Mishhu' - or any other who's job is to think - be able to go far outside the box enough to become a sympathetic character from an OOC point of view?
I would not do it, because it's not the kinds of theme I'd pursue as a GM.
Bear in mind that Wes hasn't come in here yet. I have a history of taking vague one-dimensional elements and fleshing them out, and while the result could look more credible it may not be quite what their creator intended for them. I fully expect Wes to walk in at some point and say "the wiki article says the Neo Mishhu is superior in all things and Fred's interpretation is wrong".
I'm going to at least explain my point of view.
Yamatai calls the Umbral and Mishhuvurthyar 'pure evil'. It's nice propaganda talk, but if we take a step back, everything that modeled the SMX as a military is mostly patterned after the Star Army of Yamatai.
The SAoY used limited (enslaved) bio-engineered soldiers. The Star Army of Yamatai was responsible for annihilating a handful of sentient races that were in some way opposed but unable to stand up to them. The Yamatai Star Empire practiced expansion and when they found alien races, it was either "join us or be conquered". Their prime furnisher in biogenetic engineering being PNUgen meant that the society (knowingly or unknowingly) beneficiated from harsh experimentation trials PNUgen did; and sometimes even Star Army Research Administration joined in with things like Project Sweetheart (put hundreds of nekos in a deathmatch and have them fight until you winnow them down to one survivor which will probably be superior).
Wes' characters will tell you that the Umbral corrupted the Mishhuvurthyar. Melisson will explain it as "give them free will and the ability to resist". Melisson herself admitted that the seed of hatefulness the Mishhu had toward Yamatai was something she planted because 'it was needed'.
But then, the Mishhu were still fundamentally different from the Umbral. Umbral are actually hive-colonies of small bug-like creatures whom have both psionic and the ability to altertheir shape to the point where they can fuse with each other and adopt a greater form. The Umbral have hive-minds and have different thought processes. Whereas the Mishhuvurthyar are just like us, a whole creature with a single brain and a sense of individuality. This marks them as fundamentally different from the Umbral, and - in their progenitor's eyes - better suited with living with humanity rather than the Umbral.
Reintegration was always a goal, but it still needed to be communicated that Mishhu were not test subjects or drone soldiers. Fighting is a way of communication, and in order to show how wrong they had been treated, the Mishhu were made to turn against Humanity and visit on them the same things that had been done to them. Except it was twisted, it was made worse. The Mishhu applied this "Doctrine of Retribution" vindicatively and their whole society and how an individual gained prestige amongst his peers became all about how well this was applied. Also, since the Umbral - as hive-mind creatures - did not have a good understanding of individuals, they made the mistake of believing that if Yamatai profitted from all the advances PNUgen provided that they also approved - by association - the horrific things PNUgen had done as well. Ignorance was not an excuse, and since the Umbral did not have a good grasp on human emotion (and suffering), neither did compation or sympathy enter the picture when the punishment seemed unfair.
So the Doctrine of Retribution was blanketed over all humanity. Eventually, 'humanity' stretched to 'all humanoid creatures'. We could say that then, the Star Army of Yamatai became in the right for protecting their innocent populace from an alien invasion. But, at the same time, the Umbral and mishhuvurthyar were on a punitive crusade to punish what was tantamount to an harmful 'interstellar bully'. They had compelling reasons to feel 'in the right'. To revel in the suffering they brought because the Yamataians
deserved it.
As the end of the first mishhu war approached, Melisson - an Umbral interpreter - was sent to try and get Yamatai to surrender to the Mishhu to end the war. That was because of Umbral politics. The "Doctrine of Retribution" had a finite span of time. It was not the only doctrine proposed, but it was followed in favor of not eliminating humankind and just showing it the error of its ways. The Doctrine of Retribution was running out of time and had not yielded enough results toward subduing Yamatai or securing a home civilization of the Mishhu in which they would not be thrall to another. Unfortunately, Melisson failed and rather than expose the Mishhu to more fighting for one more year (in which Yamatai showed itself ready to go for 'scorched earth' tactics to counter the SMX) she had her forces withdraw until the next doctrine could be decided on.
The next was the "Doctrine of Annihilation". Behind the drive of an Umbral Elder named Reiaz, the Umbral kind of went "fuck it, humans are not worth so much bother; we ought to just wipe them out like the harmful vermin they are". Eventually building a place-to-be for the Mishhu stopped being a goal and, based on how it had become comfortable to hate for the Mishhu, the pro-Annihilation Umbral elders had them changed into 'better' war machines. Stronger and better controlled. Being better controlled - to me - meant they'd lost something they were trying to achieve all along and that diminished them. Being a smart command-type doesn't really change that they'd only be suited for military life and that adaptation to civilian lives would require repurposing what it's made to do (prison warden?) or reduce it to menial labor (waste disposal, yay).
That's where, from the mother's point of view (Melisson a.k.a. Mefpralphra) that her own species aim in this conflict lost its 'morality'. In changing the Mishhu into the Neo Mishhu, the Umbral were becoming just as bad as PNUgen; they were becoming like their own enemy. They really were genuinely stooping down to 'evil' even under their own standards as explorers.
There are still original classic mishhu in a remnant of the SMX somewhere out there, but without Mefpralphra (majority of the body destroyed during the Miharu plot and last major surviving bits engaged/incarcerated elsewhere as "Melisson") all that's left leading the SMX are Mefpralphra's Ghost Mishhuvurthyar offsprings (Ghost mishhu heing mishhu eggs incubated under the direct attention of an umbral) such as Doshii Jun's Mefprenhel in the 44th Fireteam plot. The classic mishhu that were not drawn back into the second mishhuvurthyar war are probably something like 1/5 of the total Mishhu population. They don't go out of their way to attack Yamatai anymore, though they probably would still attack on sight most of the time (they still hate Yamataians, they just understand they cannot build a living that way). Since classic Mishhu in the past have been able to cooperate with fringe elements, I view them as the most capable of becoming part of other societies.
Again, in sort of the "D&D Dark Elf" fashion.