As I'm sure everyone knows, large parts of the Windows ecosystem have a long legacy of assuming that the end user has administrative permissions, and consequently a lot of programs work correctly only when run that way. (I'm not going to delve into that history here, nor will I entertain any finger-pointing on the topic at this time. One of these days I'll post my thoughts on that subject.) As computer security has become increasingly important, breaking that cycle became absolutely imperative. It is with the release of Windows Vista that the first major move in that direction is achieved. Indeed, the primary purpose of the technologies that comprise UAC is to enable "standard user" to be the default for Windows, encouraging software developers to create applications that do not require admin. The move to standard user is a new paradigm and creates the need for software developers to write applications that do not require admin privileges. Creating a shift in the ecosystem will take a long time due to the large deployed base of legacy applications, and UAC is a good first step.
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If it were possible to mark an application to run with silently-elevated privileges, what would become of all those apps out there with LUA bugs? Answer: they'd all be marked to silently elevate. How would future software for Windows be written? Answer: To silently elevate. Nobody would actually fix their apps, and end-user applications will continue to require and run with full administrative permissions unnecessarily.
What if the application could not mark itself for silent elevation but instead had to be marked by the consumer or enterprise administrator installing the application? Answer: the developer of the installation program (which necessarily runs with admin/system permissions in order to install machine-wide) would figure out where the setting lived, and set it. (Several major ISVs told us directly that they would in fact do exactly that.) There would be no real way to protect that setting from anything running as admin. This would be especially true if it were settable via Group Policy (which would be expected, if not demanded).