There is currently only an option to "Don't publish directories" in the Publishing filter. To be able to specify a list of "Directories to publish" would be helpful. This may also help the Smart Sync be faster, - if it has a list of folders to scan (and their subfolders), rather than scanning the entire directory tree. For a Laravel project especially, it would be more useful to be able to specify a list of directories to publish.

Also, I can't figure out how to get smart sync to run faster (with "Use cache" turned off). Even if I exclude all top level folders in my Laravel project, except for the /app/ folder, the smart sync takes a long time to scan. It seems like it must be scanning every file in the entire project, and then applying the filter to each file. I'm just guessing, since my /app/ folder contains only about 20 files and a few sub-folders, but the smart scan takes 2-3 minutes.

Right click on folder in Workspace project tree -> Properties. It's where you can prohibit publishing this directory and add Allow/disallow masks for the files/subfolders in it.
Same filter is in Project's properties -- it's for the project root directory. Allow/disallow filter is applied for both folders and files.
RE performance -- I guess you're using FTP. If so, try to switch to SFTP or webdav. They work faster. Samba in some cases may be fast enough too. FTP won't work fast anyway. To send content of each directory it has to open new data connection which is closed as soon as it is finished.