It sounds like you may be facing a known issue with the Windows Mobile SDK 10.2:
NIM097317: A "Missing ArcGIS Registry Key" error occurs due to a registry key mismatch.
The current workaround is to create a new registry key, Mobile10.2.0, at the same place as the Mobile10.2. Here is an example of where that should be found:
(old) HKEY_LOCAL_MACHINE\Software\ESRI\Mobile10.2\InstallDir
(new) HKEY_LOCAL_MACHINE\Software\ESRI\Mobile10.2.0\InstallDir
Note that you must change the registry key on the Windows Mobile device as well.
Hope this helps!
-Noah