Yeah, I also didn't care for the glory kill indicators and their function as much in 2016 either and also think they work much better in Eternal, like the concept was more properly executed, mechanics-wise.I didn't like them in 2016 and had them off. I don't really like glory kills in general, and mostly avoided them in 2016. I'd only do a handful every level.
But in Eternal, the game seems tuned around them quite a bit, so they're much more important to use. And because everything is so fast, the visual highlight is important. I didn't like it at first, but I've gotten used to the new routine.
I do appreciate that they seem to somewhat lose importance as the game goes on, both because you get enough firepower to kill enemies without them, and also because there's so much crap thrown at you that it makes sense to pass up glory kills in many situations.
I just wish the highlights were more diegetic to the game experience itself rather than the obvious flashing, "kill-me-now" highlights. I think highlighting the staggered demons is necessary because like you say, the game's pace/intensity is so fast that you need them to standout, especially because glory killing is crucial to staying alive.
I also was a fan of them giving more avenues for health recovery as you progress with the ice bomb kills and blood punches being ways to recover HP.
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Regarding the story in Eternal, I definitely think the story should be far more minimalist. They clearly took a bunch of inspiration from Super Mario with Doom Eternal, but one of the big things I feel they should have really took from Super Mario was the narrative. All of the Mario games' stories are the same: Peach is kidnapped by Bowser, and Mario has to save the day. That's it, and it doesn't need to really be anything more IMHO. Same kind of thinking should apply to DOOM: Demons have shown up to mess shit up and now Doom Guy just has to kill 'em, nothing more is necessary.