With the high specs, low price, ease of use and and uncomplicated setup of the new generation of consoles, will the PC no longer be the platform of choice for gaming?
I don't think so on any of the counts. For the most part, the games people play on PCs aren't the same style of games as are played on the consoles. People have been predicting that consoles will overtake PCs for several generations. Yet PC sales are as strong as ever.
And as PC hardware upgrades are largely determined by games where does this leave the future of the PC in terms of hardware advancement?
Well, I think the biggest threat here is that video card manufacturers may be pricing themselves out of market. Who exactly is willing to spend $800 (two $400 SLI cards) to have the greatest video for 6 months until the next gen chipsets are released? I might expect to see video card development cool down a bit. But that's not really related to your question, and honestly, I don't think it'll matter a bit. As Longhorn (or Vista or whatever it's called this week) will dictate plenty of upgrades and new systems sold.
Ditto for Microsoft?
Why would it matter to them? Outside of DirectX, has Microsoft ever done anything to attract game companies to come to Windows? Their market is e-mail, web browsing, and office. Offering some new glitter features and a promise of more security should be all that is needed to get the masses to update.
Is Nintendo dead either way?
I don't think so. They'll remain as a niche player. And, with their strange innovations and such, they will distance themselves from the XBox 360/PS3 war coming up.