The Remote is quite simply, the cheapest and least capable way of using the system.
With this said,
The USB UIRT can recognize almost any remote control. However, we only have device templates for the standard MCE remotes. So the MCE remotes will work out of the box, any other remote will require reading the "support for new remote controls" document on the wiki.
The USB UIRT also gives you the ability to do IR learning, which is essential IF you have an A/V device that does not already exist in our database (we have pronto codes for most manufacturers and controls, and they are very much interchangeable between them, and as part of creating new device templates, you are given the opportunity to test pronto codes that may match your device.).
Keep in mind too, that we do have the Orbiters. I would suggest looking into this software for control as well, as it is shipped with each and every copy of LinuxMCE, and is the most capable control out of the bunch.