Hi Simon,
We originally made the decision to go with ClickOnce primarily for the ease of deployment and the automatic updates. In retrospect, it wasn't the right choice and we are currently looking to move away from ClickOnce, to a standard Windows MSI installation. There are a number of reasons for this; occasional, difficult support issues when ClickOnce installations fail, inability to produce proper standalone installers for CD distribution and some issues around localisataion (planned in 2014). Unfortunately, the transition is not totally straightforward (or we would have done it already) and, in particular moving the current user-base across automatically will be a challenge. As it happens, ClickOnce won't let us update users from the current 32 bit release to an AnyCPU build that supports 64 bit. We have this build in beta now, and it offers advantages such as much bigger maximum map sizes, so introducing the 64 bit version will probably be the factor that finally forces us to make the switch. Expect something early 2014.
Matt