I agree this is a mess. While I haven't been able to figure out a GOOD workaound, I do want to tell you about something you can do if you're so inclined: use symbolic links (also called symlinks). These are similar to aliases but the difference is that whereas the Mountain Lion screen saver ignore aliases, it works with symlinks (in the right circumstances; I'll explain more below). Also, symlinks are vastly smaller than aliases (why the heck are aliases so dang big?!?) which at the scale we're talking about here might actually make a difference.
Symlinks can be created with Terminal and if you Google you'll find more information on this. But I recommend making your life easy and using SymbolicLinker. I'm going to go into more details about how to make this work in a moment but before I do I need to expound on my comments above about the Mountain Lion screen saver symlinks working "in the right circumstances." As well as I can tell, the Mountain Lion screen saver will work with symlinked files that have names that appear to be image names. In other words, if a file has a name like "myimage.jpg" (without the quotes of course) and it's actually a symlink, the Mountain Lion screen saver will work with it (and again, this is NOT true for an alias: I have found that the Mountain Lion screen saver won't work with an alias named something like "myimage.jpg" nor will it work with any other aliases). However, I've found that if the file has a name that does not appear to be an image--such as "myimage.jpg symlink"--then it will not work. And names like "myimage.jpg symlink" are exactly what are produced by SymbolicLinker. So you'll need to change the names of these symlinks before the Mountain Lion screen saver will work with them. And for that, I recommend NameChanger.
Okay, so here are the steps:
- Create a directory to which you will point the Mountain Lion screen saver (to keep things clean, this should be something other than Pictures and it should be used only for this purpose but it's up to you; I recommend creating a directory called "Screen Saver" inside your Pictures directory).
- Go to one of the directories with photos you want to use with the Mountain Lion screen saver and select all the photos you want to use with the screen saver, right-click, and choose Make Symbolic Link.
- Sort the finder window by Kind and select all the items of type Alias (Mac OS X dubs your symlinks aliases but remember, they're actually symlinks, not aliases) and drag them to the directory you created in step 1.
- Repeat steps 2 and 3 for all other directories with photos you want to use with the Mountain Lion screen saver.
- Open NameChanger.
- Go to the directory you created in step 1, select all items, and drag them into NameChanger.
- In NameChanger, type " symlink" (with the space, without the quotes) into the Original Text box. You'll see the file names in the Renamed Filenames column are changed to remove the " symlink" part.
- Press Rename.
- And finally, point the Mountain Lion screen saver at the directory you created in step 1.
Again, this isn't perfect: if you move the source files, the symlinks to those files will break and plus the procedure above can take a while to do, not to mention that you have to perform this procedure every time you want new pictures to be known to the Mountain Lion screen saver. The only way around that would be to create a utility that would watch a directory (such as the Pictures directory) and all its subdirectories and would perform the equivalent of the above steps (well, just 2 through 8 really) whenever a new picture was added. Unfortunately, I do not know of such a utility.