Make sure Microsoft Visual C++ 2015 Redistributable (x64) 14.0.24215.1 is installed before you start the silent install otherwise it will fail because installation of c++ 2015 is not silent in the installer.
MeshLab2016.12.exe /S
it should be
"%ProgramW6432%VCGMeshLabuninst.exe" /S
but it is broken. Dialogs are popping up.