The biggest benefit to using C2R is that whenever you click the link (which downloads the application’s manifest file) you get the latest version of the HCW, streamed directly to you from Microsoft’s servers. The Office 365 team (hi, Tim Heeney!) made the wise decision to turn it into a Click-To-Run (C2R) executable.
The HCW used to be a standalone Windows executable that you’d download. Hopefully this article will be a useful breadcrumb for future hybridizers.
I recently ran into a bizarre problem with the Office 365 Hybrid Configuration Wizard, and solved it after a bit of trial and error.