I want to restate that complaining about Alisaie's character does not mean I want to get rid of her in any way. I'm mainly just trying to figure out why and how the story so far has shafted her this badly, and how it could be changed to make her a better character. Killing her off now would honestly just piss me off even more, because that pretty much means giving up on fixing the issues that her presence has caused.
As it stands, it feels like she brings very little to the table if she's not the awkwardly-shoehorned main star of a patch. A quick examination of her actions throughout 3.4: Shows up after taking an arrow to the shoulder or something, recovers after... a few days? Then completely overcompensates for her weak reintroduction by becoming a mechanic for a showdown between the WoLs and WoDs that's been anticipated since 3.0.
(Yeah, this is exactly what I wanted, an epic fight being reduced to "Touch this NPC so they can win the fight for you and completely defeat the purpose of being the WoL!")
At this point I just want to say, the writers can dress her up, give her all the minions, and make her as OP in fights as they want, but Alisaie's not going to be an important or compelling character until she starts actively affecting the plot the way every other Scion seems easily capable of doing. I will freely admit that Yda* greatly annoys me as well, but I'm not complaining about her because she still manages to be integral to the plot.
Perhaps the problem just lies with Alisaie's motivations. The main, overarching plot is one of people fighting and dying to save the world, and this drives their every action. Meanwhile, all Alisaie seems to care about is Louisoix, or forging her own path based on Louisoix's ideals, not her own - and it says a lot about the twins when Alphinaud clearly cares more about her than chasing Louisoix's memory, which, yeah, is one reason why I prefer him - and this just doesn't tie her into the main plot very well.
So compared to the rest of the cast's relatively selfless goals, the fact that Alisaie's goals and motivations are largely self-centered just makes her come off as really irritating. There's also the fact that her seeming eagerness to kill is a bit creepy to me. She just seems way more bloodthirsty than Alphinaud, for reasons I can't fully comprehend.