Are you on Windows or Mac?
On Windows, the old pre-Vista folder browser is pretty bad. I'm replacing it with a more modern folder browser right now. This will be included in v4.5 for Windows.
In the mean time, there are some tricks to make this easier to work with. Did you know that you can type - or paste - a folder path into the Gather Project window? You might not need to use Choose Folder at all.
In some cases you can even type in a folder that doesn't exist yet, and it will automatically create it when you start the gather process. This only works if it only needs to create one folder; it won't work if it has to create folders two levels deep or more.
If you keep a Windows Explorer window open in the root folder where all your gathered subfolders are, you can copy and paste this in every time and just type the name of the new subfolder, then go straight to the Gather Project and Assets button.