Mike,
Conceptually, I understand well the difference between building a windows WPF application with the ArcGis Runtime component and customising an ArcGis Explorer with add-ins. However, the end result for the user is similar.
I have chosen ArcGis Runtime because I am building a WPF user control that will be used as a dll component that can be reused in other projects and that interact with other user control (chart and table) that are spedific to hydrology. Our chart and grid are more advanced that the one available in ESRI widgets. These 3 components are part of a decision support system. Basically, I am wrapping ArcGis Runtime and build a dll component. I am not making an executable.
Having said that, there are very few peoples that have the skills to build software component and they will probably chose the ArcGis Explorer customisation which requires less effort. The most important question to me was: Is there any plan to support "mpk" with temporal data for ArcGis Explorer. If this is the case, I wonder if I would be better stop working on my software component and use ArcGis Explorer instead because I am afraid everybody will follow the free ArcGis Explorer solution instead of ArcGis runtime. That would make ArcGis runtime solution obsolete.
François