Okay, so, with Copen sparing Blade in iX1 and all bosses of GV3 being spared, it would bring someone of the other bosses being sparable. However, while I can find it with the bosses of Gunvolt 2 and iX 1 (except Crimm because fuck him), and the choice with the iX 2 bosses is mute, as Autochrome states in his fight (he alludes to how you've fought Vespa beforehand, and mentions that Workers can be repaired even if they're killed, so he has no hard feelings for you killing his sister), for GV1, only Copen and Elise are worth sparing.
So, first, I have to get Copen out of the way. iX proves Copen can learn not to think Adepts are Always Chaotic Evil. In my opinion, he not only can, he has to. Which is why he needs to be spared.
Elise is the main point of this post. The reason she needs to be spared? First off, she's the only Sumeragi Swordsman who can: Stratos is too far gone, Zonda prefers being lumped in with the Gunvolt 2 bosses so she doesn't count as a Sumeragi Swordsman, and everyone else is an asshole; Nova claims you should just submit to Sumeragi and let them abuse Adepts forever, Jota is fanatic in his belief Sumeragi are the good guys, it's all but outright stated Viper wants to rape Joule, Carrera openly states he only cares about greed, and don't get me started on Merak. Meanwhile, Elise is meek and timid; she may have a dark side, but it's nothing that can't be fixed: it was caused by people treating her as a monster because she was an Adept, and even then her timid nature keeps her resentment of normal people, which is the true nature of her dark side, in check. (And then Merak let it loose...) If she is given the chance to have a happy life where she's not persecuted, her dark side would vanish in time.
Also, her Septima is capable of preventing Asimov from killing Joule, which ends up causing everything bad that happens in the rest of the series.
I also looked into the game itself, and I found something interesting when fighting Elise: if you focus to kill only one half, the other won't start using Ressurection right away, only when she's been damaged enough. And even then, the Elises only use Ressurection five times (at least in the initial fight; I didn't get far enough in the game to test if Crazy Elise's Ressurection restores the Ressurection count of the other two, but that doesn't bear much to my point). The point is, they wasted a perfectly good plot: why didn't they make it so killing Dom Elise without laying even a single tag on Sub Elise would allow you to spare Elise, which unlocks a different ending?