"Another difference between ISVs and Web sites is in the type of developer they employ and the assumptions those developers bring to the table. Rarely do developers at Web companies have experience creating interactive client applications; nearly all of the developers at Web companies are server developers, and the people working on the user interface are closer to page designers than developers in terms of skills. It can be difficult to push a front-end Web team (used to building pages, not applications) to work as software engineers on interactive client software; but that is what is required when building real-world RIAs. Software developers at ISVs tend to have the perspective required to understand this; over time, we expect Web developers to arrive at the same place, but for different reasons and from a different starting point.
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You need the right combination of skills if you’re thinking of delivering an application both as a (HTML) web app and as a RIA (say, by combining Flex with a Java backend/framework). Those worlds will indeed merge eventually.