The web version is intended to augment the desktop version, at least for quite a while, providing support for all the other platforms that users want to leverage. We first need to get the web version launched for players. Then we'll be putting out a version for GMs that is targeted at running game sessions, allowing GMs to use whatever device they want for that purpose. Then we'll need to get all the world building stuff into the web version, which is a LOT of functionality.
So it's going to take quite some time to ultimately get the web version to the same level as the desktop. By that point, internet access may be so ubiquitous that it makes sense to phase out the desktop version, or the desktop may still be necessary. I have no idea, and anyone who asserts otherwise is making rash assumptions about the future. So we'll just have to figure that out down the road.
EDIT: The bottom line is that the desktop version is going to be around for quite some time still.