I agree Deus Ex was kind of a peak for pc gaming. But one reason is because that was the last of the "PC Exclusive" games before everything started simultaneously being released for consoles. Consoles which need a 10 foot interface and are limited to 8ish buttons and the short attention span of the console players.
However that isn't a reason to despair. Look at STALKER which was released 7 years after DE. It doesn't have the npc complexity or story branching but it does have the same kind of open world immersion and quirky gameplay that made DE and System Shock 2 so memorable. And hey that was a PC exclusive as well.
I think with Steam and the price competition for .99 Ipad games there is a renaissance of PC gaming on the horizon. There are a ton of smaller, memorable, lovingly crafted games indie games available from Minecraft to Gratuitous Space Battles, to E.Y.E: Divine Cybermancy which really is a spiritual successor to DE1.
Even venerable Dwarf Fortress, the granddaddy of quirky, do whatever the hell you want gameplay, got a major update a few months ago.
So the future is hopeful and even thought the AAA landscape may never produce another DE the spirit lives on.