More and more head units come with an infrared remote. They make a wired infrared receiver (used in media rooms where the equipment is hidden) that's little more than a black tic-tac. You could incorporate it somewhere on the dash, and simply run the wire to the trunk where you can have a box to hold the equipment. That would allow you to control your equipment via the remote without actually being able to touch it and if you also have an Ipod, you won't need to access it to change CD's.
Put 3 1/2" midrange/tweeters into your dash corners (or together on a plate if you only have the center 4x10 opening), use the 6x9 factory openings in the package tray and place a small box firing towards the rear seat. Better yet, port it through the defroster opening. This can leave it absolutely stock looking on the inside and still provide modern tunes.