It basically makes a special-case out of a specific template. This is like saying "if you see a program that does X, instead of executing it, execute something else instead".
No, not "something else", it is "if you see this very-specific sequence of bytes in the scriptPubKey then do this ADDITIONAL validation."
As for saying something in BIP 16 about obsoleting scriptPubKey : no. Although I think in the future we'll move towards all transactions being pay-to-script-hash, I think it is dumb to put anything like "we think this is what is going to happen in the future" into standards documents.
Can we keep the big picture in mind? The reason I'm pushing so hard for "send bitcoins to a multisignature-protected-address" functionality is so users stop losing their bitcoins to malware infecting their computers and smartphones and to scammers.
We can spend more months arguing over trivia, but I would much rather we spent the time thinking hard about, and building, great wallet and escrow solutions that solve Bitcoin's biggest technical problems.