That said, story is but one element of a video game. Most are praised for their gameplay, but some are for their aesthetics (Hollow knight, bastion), music (transistor), or others criteria. Thus, a game that excels at none can sometimes come on the top... But so can other games that all but stopped trying scoring on some aspects (dwarf fortress, or doom).
Normally I agree with the GP, and prefer the joyously silly/unashamedly dumb approach over the 99.9% of more 'serious' games that are tediously mediocre at best. And on paper Deus Ex should have been pretty annoying: it is a slightly janky mix of lowbrow conspiracy fiction and quasi-highbrow philosophising. But somehow -- obviously partly because of the still-fresh-20-years later gameplay, but also because of something I can't quite pin down in the synergy between gameplay and story -- it works amazingly well.
It really nails the feeling of existing in and shaping an exciting world, and I think every component is crucial, from the (blocky) environments to the (ludicrous) characters to the (somewhat awkward) mechanics, and of course the 'every conspiracy theory is true' plot. Obviously it has a sense of humour too, but I don't think it would have worked if it were constantly taking the piss out of itself.
SOMA, SOMA, SOMA. The best story I have ever seen in any videogame, ever.
Heck, Half Life looks like a -mediocre- episode of The Outer Limits.