Just keep in mind that using an aftermarket panel doesn't mean you have to replace the entire panel. If the rust is limited to the bottom of the wheel house, you can section out the bad metal, cut the replacement panel to fit the gap and weld that in. If you do a good job of fitting, welding and grinding it down, you won't be able to see a seam afterwards.
Once you get into the quarter panel, the might-as-wells could cost you more and more. You could use a magnet to figure out how much bondo is there.