Without hearing about specific workflows, this can't be answered very well.
Here is my generalization. ArcPad is a more thoroughly thought out product that has been developed over quite a few years. Compare that to the relatively new ArcGIS Mobile for Windows. For complex data collection, ArcPad is not great but I have not seen anything better. ArcGIS Mobile for Windows adds what may be unneeded complexity of moving data back and forth with ArcGIS Server.
With the recent changes in ArcGIS Server licensing and attempted forced integration of ArcGIS Online, who knows what ArcGIS Mobile for Windows might force an organization into. Currently ArcPad does not suffer from these problems.