Would you please consider changing your Live Update system to one that gives the customer a choice between checking all files and simply pushing updated files to the system?
That's exactly how the Live update does right now. It "simply push updated files to the system" but, of course, in order to know which files are outdated on you system, it must check each one.
And yes, it's already done in the most efficient way possible: by storing a cache of all files MD5 locally and comparing it with the same cache file on the server, so it doesn't have to go through each file on the server, which would be very slow indeed.
It's not really possible to do what you are suggesting, like dividing between "important" or "bugfix" files, and "just updates", like new objects, graphics, etc. because sometimes they depend from each other, and if you were allowed to choose which one to update, it might result in errors like not finding an object, because you asked to update the code that calls it, but skipped the object itself.
