What I saw people complain the most about, here and elsewhere was that
1) Doom Eternal had a lot more stroy and it was bad. The story was not good, yes, but the notion that Doom 2016 went with "fuck story" is mindboggling since it was everywhere and cutscenes were unskippable, whereas in Eternal, you can pretty much skip everywthing and not even know there is a story at all.
2) no ammo - I saw people surprised by the fact that the chainsaw regenerates, which is the typical "user fails to read basic short text and then blames the programm" scenario. The game has pretty much infinite ammo, the second I learned to use the chainsaw was the second any and all ammo problems dissapeared. The fact that you can't just SSG your way through the game as you could in 2016 ties also here, while the SSG in 2016 was great, there was little reason to use anything else. Eternal is designed so that weapon cycling is encouraged, I can't see that as an disadvantage.
3) Doomguy in Eternal is not a power fantasy - This I don't understand at all since Doomguy wrecks shit even harder than in 2016. The one difference is that you have to move and can't stand around tanking all the damage, which I consider a good move.
4) You have to use certain weapons on certain enemies - Another one I don't understand since the only enemy you sort of have to use specific weapons on is the Marauder (in the base game, the dlc adds an enemy you have to use one certain weapon mod on), and the Marauder became easier the more one played. In the DLC they became a non issue. As for other enemies, some of them have weakpoints, yes, but I don't understand why some people act like it's mandatory to shoot them, I never bothered, except for the begining of the game, but a few levels in, when you have more options, it's a completely optional feature, depending on if it fits a playstyle.
I'm sure there was more, this is just top of my head. One funny complaint that came up from time to time was that the ammo showers are too colorful and you can't see anything. I wonder how many of those people bothered to go to the game options and reduce the color intensity on those.
My personal strong complaint is that the Battlemode sucks and I wanted the game to have normal deathmatch. I guess they didn't include it so that Quake Champions can still exist but it's a shame either way. But outside of that, there's little I can see as a negative. The story got weird, but it's Doom in the end I don't care, I still have Doomguy who wrecks demons, that's all that's needed really. As I see it, the took Doom 2016 and made everything evolved and better. I hope they can do the same in the next one.
