Prey 2017 was fantastic.. but in terms of ambition it was a step back, it's basically an improvement on system shock 2.
I do think there is an ultimate game out there that has not been made yet.. We could do it now though, combine a totally open simulation like minecraft with on-the-fly story / dialogue / characters by an LLM.
I'm not sure what you mean by ambition. Deus Ex was pretty heavily criticized for having "last-gen" graphics
What made Deus Ex stand out was the writing and atmosphere, and maybe some gameplay mechanics which hadn't become quite so popular. As you mentioned System Shock had already pioneered them, although that game didn't reach the level of popularity of Deus Ex which won game of the year in 2000
I'd also add in the music, to this day I still remember the main theme. Alot of games these days, don't even bother.
I would argue that games like Cyberpunk 2077 or KCD2 are a logical step-up for the genre offering open world, next gen graphics, many more weapons, NPCs, interactions, etc. and quite ambitious.
Same could be same of Skyrim 10 years ago.