So, when I mention the Assassin's Creed / Far Cry / GTA triangle I really mean to say the poor imitators of those games. They did do some very innovative things when they first came out, but just like modern military shooters took regenerating health and the two weapon limit from Halo while leaving behind all the other gameplay mechanics that made that work, so too did many games adopt the open world and the general way you interact with it, while removing anything interesting. By "the way you interact with it" I'm referring specifically to the map unlocking, the collectables, the village / territory faction control, and the "heat" system that spawns enemies depending on how much attention you are generating.

IMO those sorts of games were very much the other side of the coin from CoD-likes, and the problem was that while the extremely linear levels of CoD-likes were too restrictive, these open world games had no structure at all. In games like Blood, Quake, or what have you, encounters are designed to flow in a certain way, with each one having its own flavor and favoring certain approaches over others. In some games you can even think of enemy encounters as a puzzle you need to solve. Level design and enemy placement of course form the two halves of encounter design. In good games this sort of thing extends to the structure of the game as a whole, with the ebs and flows in the action, and different gameplay happening in different sections so the formula keeps getting changed up. But in games where the level design is an open world that let's you approach from any angle, and where enemy placement is determined on the fly by a mindless algorithm, there is no encounter design. At the same time the way enemy spawning works is actually too orchestrated to have interesting emergent gameplay. For example, if an algorithm made an enemy patrol spawn an hour ago, and the player can see it from across the map, they can come up with their own plan on how to deal with this unique situation. If the player gets one bar of heat and the algorithm makes an enemy spawn around a corner they can't anticipate that at all, its just mindless. This has implications for the gameplay itself (no enemy can be very tough or require very much thinking or planning if you're just going to spawn them around a corner) but also, as previously stated, the entire structure of the game.

As for the other games you mention, I want to bring up Bioshock in particular. Its true, that game is a master class in presentation and aesthetics, and a game I would highly recommend, but its actually one of the games that I remember people complaining about when they said gaming was better in the 90s. Specifically the way Bioshock is very dumbed down compared to its predecessor System Shock, both from a general game and level design standpoint, but also because of the inclusion of vita chambers and the compass pointer that leads you around by the nose. (One place I will give Bioshock points though is that it has way more of an ecosystem than most imm-sims with the way enemies interact with each other; it even beats out imm-sim darling Prey 2017 in this regard).

This is admittedly a way more niche complaint than people complaining about QTEs or games being piss/brown, but it was definitely a smaller part of the much larger "games are getting dumbed down" discourse.

I could talk about Crysis and Spore too, but this comment is already really long. I haven't played the rest of the games you list, so I can't offer an opinion on them, though I have heard that KOTOR was very good.

You're right, as is so often the case when people talk about a decade I'm thinking more of its latter half and the beginning half of the next one.

But in my defense I did say "the mid to late 2000s".

I have a few more thoughts, but I'll have to make another reply in a bit.