Premise: The more indistinguishable a browser gets from its underlying operating system the more of the properties of said system it must share. Thus stretching the nature of the abstraction, making it shallower (till the machine) hence also increasing the probability of leaks in said abstraction.
In particular, as margins from speed, ui and features decrease; each vendor will become incentivized to avoid commodification and distinguish themselves from their competitors by moving faster than the glacial speeds of standard bodies and introducing incompatibilities. While being slow to pick up those of others. In essence each browser would basically evolve into and become indistinguishable from a current OS with all its pitfalls (isomorphic rather than homomorphic as currently). And if we are targeting specific VMs then we may as well factor out the browsers as they are no longer a vital component of the equation. Completing the cycle. To be restarted with metabrowsers.
Seems to me that pushing for native into the browser without carefully considering the tradeoffs is foolish. You cannot have uniformity without sacrificing diversity. This seems like the original Java dream rebooted. But it seems to me that wanting the same UI and code to work everywhere while taking advantage of underlying hardware, while automatically adapting and falling back on visuals and optimizations is a pipe dream. That is of course, until OS's and programs become intelligent and partially alive. At least microbe level intelligence. And virus like adaptibility.
Aside: NaCl appears to have a decent amount in common with silverlight. Particularly in terms of tradeoffs, weaknesses and gains.
And then my opinion that browsers will evolve into the platform and not be separable from the OS. Stuff like NaCl simply accelerates that by introducing a dependency on one company or creating a technology that invites splintering on implementation due to its complexity and uniqueness.