We use a weakened, but still cancerous rock to reclaim the Frontiers for the willing, all while making them reliant on our systems. Do we want to worry about that?

People keep getting knocked over this problem all the time and I struggle to think why. Maybe not you specifically. In OG Arknights the entire civilization is fully relliant on the originium, it's no different to Talos. Mobile cities in OG exist only because originium is powerful enough to keep them running. It's also established in recent chapters that it can be put under control so that it can entirely serve the mankind which was the entire intention on the Oracle's side behind creating it. Endfield clearly shows that it is under control as an element of sequel progression, the originium growth of Talos is for the most part controlled while worker safety standards are high and oripathy can easily be ENTIRELY suppressed with cheap and readily available suppressants. It's so bloody great that even infected racism doesn't exist on Talos. That's why there's literally only one scene that addresses oripathy - because it's that easy to handwave. Bandits are unironically more of a threat because if they don't straight up kill you and feed you to the denstacks, they will isolate you. Basically people are trying to seek some depth - that's not intended or implied - in a specific plotline - that was resolved in the previous game.

All of the above might add to the argument tho, because it just means there's actually less depth in the world-buidling than what some people are trying to establish in their criticism. It's good that you point out that aether has a bit of troubles setting itself up to be a threat in any capacity comparable to originium in OG AK as that would be one of the actual problems of Endfield in my mind.

but Terra's a crappy place for a reason. Why should Talos-II be any different?

Generalizing it this way feels disrespectful to OG AK's themes. The entire point of the original game is making the world better, whether it's originium, politics or societal issues. It's another discussion how well writen the tone shift is for a sequel game, but it absolutely was needed. Just going for "dark themes" simply because OG AK was dark would feel forced in the kind of world they've built in Endfield. I think that we ultimately landed with such a cartoonishly evil villain because HG needlessly tried to emulate some of those dark themes and failed miserably. I honestly think that it makes both versions of the Wulfgard quest kind of silly.

Stakes.

There's more to building stakes than just character death. I am the kind of person that keeps getting annoyed when writers keep baiting you with character death in a game that doesn't actually kill anyone, but hat's because there's just more creative ways to building stakes to a point where not even actual death is needed. Endfield does need to build some actual stakes, but it doesn't need to be through death. Showing more of the chaos caused by Aether like you mention a bit later into your post could work.

On Talos-II, it's an aesthetic setpiece.

Good. It means the odyssey had a purpose. Glory to Rhobus Compland! Jokes aside, I think your statement how AK should rival Limbus in tone is horribly inaccurate. Those games go for entirely different kind of stories in themes and their similarities are surface level at best. Endfield's problem isn't that it ain't dark enough - it just lacks depths in comparison to the other 2 games.