Well, if I'm understanding the article correctly, then when you boil everything down, it would seem that, deliberate or not, the MS O/S is our primary boat-anchor. I've spent a fortune on system upgrades in the last 9 months. I'm just now reaching the point where I'm getting satisfactory performance out of this years games. It would seem then that if the PC O/S cannot or will not be formulated to take advantage of all this horsepower, maybe it's time for an indy to step in and formulate an O/S that can be dual booted and which will focus exclusively on game app performance and communications. Can't say there wouldnt be a market for it.
Well, there is only so much that can be done from the operating system standpoint.
The OS still has to have an API that serves as a common interface to the video card drivers, which then translate instruction so that they work on the 3D hardware.
This process can probably be improved and tweaked such that it takes better advantage of the computers hardware over time (particularly multiple cores) but a lot of this lies with the developers of the 3D engines the games are built on as well, to make sure their engines are multithreaded.
In the grand scheme though, the reason a console will always be faster, if running on equivalent hardware is because every one of that brand of console has the same hardware.
The console game engine can natively speak to the GPU, whereas everything on the PC needs to go through the combination of Direct 3D or Open GL API's and drivers which act as translators between the game engine and 3d hardware. This real time "translation" is what causes the extra load.
Another benefit the console has is that when you are making a game for a console, you can optimize each scene for your one hardware configuration, and test it, and know that it will be representative of what all users will experience. On a PC you can't really do this.
The developers could say "Hmm, having 7 buildings in this scene makes the game render kind of slow on console X, so we are going to put in 6 buildings instead". In more detail they can optimize it to the amount of VRAM and GPU power present. With a PC you have to choose one configuration and stick with it, and all sorts of different types of hardware which it is not optimized for will run it.
If every single PC had the same CPU, the same motherboard, the same type and amount of RAM, the exact same video card, and the same output resolution, you could overcome that gap, but this is not going to happen. hardware diversity is one of the things that makes the PC platform great.
But as mentioned before, it is a moot point.
Current consoles are a snapshot of ~2005 mid to high end hardware. Compared to PC's today, they are all but obsolete. The hardware commonality benefits allows them to still remain somewhat relevant, but they are still outclassed by the brute force of PC's.
So, when the next generation of consoles are released. (2012? 2013?) they will be a snapshot of mid to high end hardware available then. But guess what, a year later, PC hardware will once again be superior and able to power through any benefits the consoles get from hardware commonality.