Even when you don’t kill Vedran or usurp Elya or tell Mira to KHS, she’s mentally clocked out in her epilogue and is effectively waiting to die (and is hastening that with her booze consumption). Probably due to grief, regret, and the pathetic trajectory of her life. And even if Elya loves her mother, she doesn’t take every word out of her mother’s mouth as a command—her canon familial love of the Marshal is the prime example of her disobeying Mira, and it took place before she had a Strength stat.
She doesn’t know how to deal in a healthy or constructive way. She’d been some level of functional alcoholic since the Marshal’s existence was revealed to her (and it’s not confirmed that she did lay off the hard stuff during her pregnancy with Belos and Vedran), and she drunkenly dishonored the Marshal immediately after telling Sobik she’d go public with the information about the Marshal’s true parentage if he didn’t disinherit the Marshal—truly a long campaign of subtle manipulation there.
As for Marshal’s power in Ending 3, there has been many an essay written on the topic, and the consensus (as well as the author’s word) is that it’s not the best for Kanton, and probably not great for the Marshal (and if things do get better for Kanton, they will be much worse first). Is it a good and interesting story though? Absolutely!
Even warm Elya is furious and unforgiving of Vedran as she reminds him that he could die for his treason (which can mitigate the kinslaying accusations, especially if she and the Marshal state that Vedran “shot first” but even then it’s a bad look) and only her grace ensures he lives, when she and the Marshal confront him in the cells, for the fates he nearly doomed them to at Rade’s hands.
If she dies at Rade’s hands in Book 2 after Ending 2, the Marshal is very likely dead already (it does sort of happen like you’re saying in Ending 1, although that takes place in Book 1). If the Marshal isn’t dead there’s a succession crisis within a succession crisis, and very likely Rade is in a stronger position (you’re sort of describing Ending 4 of Book 1, the only ending carried forward that has a canonical outcome for the final battle—a retreat of the loyalists).
Here is the way to get Ending 2: either win, stalemate or avoid (Tactics guerilla campaign route) the final battle with Rade, or retreat with Elya at Strength 4 or more (lower strength gives you Ending 4) and without sacrificing yourself (doing so gives you Ending 1) in Chapter 9. Then don’t usurp Elya in Chapter 11 (keep your Envy below 4 or take any one of the off-ramps to the usurpation plot, starting with not secretly talking to Archbishop Wrido. Doing neither of these things gets you Ending 3), and witness her coronation. While many people, myself included, will carry forward a victorious outcome in the final battle, it is not a canonical part of Ending 2.
As for Elya’s weakness and vulnerability to assassins: go out and personally join the fighting during the Battle of the Atiming in Chapter 5 without attacking the rebel camp first, when Elya has Strength 4+.
I don’t remember him saying we can become ruler of Kanton in Book 2 if we don’t start as such in Book 1. Krorid is fair game and there are hints in Book 1 about the Marshal possibly becoming ruler of Independent Krorid (but nothing comes of it in Book 1 since the Marshal is dealing with Kanton’s succession crisis first) in Book 2.
Wasn’t talking about Vedran. This is Drazen, who wanted to become rich and gain notoriety by killing the girl queen, in the middle of the actual battle, and got her to put her dagger through his neck for his trouble (and unlocked an achievement for the player in the process).
Elya does have guards such as Velinor (who we see smoking people that try to kill him, and confirmed as no slouch in close combat). And he does send an assassin after Darin in Chapter 8–a turned ranger who sees an old man recovering from new injuries and thinks the job is easy.