The analogy to IE6 is based on both requiring substantial duplication of effort in order to render the page similarly to its appearance in other browsers and to provide like functionality to web sites. It seems to me that in part, Apple's intention is to make it less troublesome to develop and maintain an app than it is to develop and maintain a rich media website which handles iOS gracefully through the deliberate incorporation of incompatibilities in the iOS browser (e.g. no Flash).

[edit] incompatibilities are different from non-compliance with standards.