Although the start-up document enables you to customize certain items in your new documents, you’re limited to one start-up document (well, two actually: one for RGB and one for CMYK). If you’re really clever (and of course you are), you can simply use multiple documents as your start-up documents, without having to swap them in and out of the Plug-Ins folder.
Try keeping a folder full of seemingly empty documents that contain special sets of styles, swatches, brushes, and layers. When you open one that has the stuff you want, choose Save As. In effect, you get a custom document, without the process of loading or creating any of the styles, swatches, brushes, or layers that you’re using.