I removed the rear pods and cut out the factory 5" mounting flange so that there was a square opening. I then used Liquid Nails to glue in a square piece of 3/4" MDF with a 5" cutout for a 5.25" midrange speaker (hole smaller than actual cone diameter). Not a lot of work and the end result is awesome. This also allows you a wide range of cheap component (or coaxial) speakers to choose from. I ordered a $45 set of Blaupunkt components off of Amazon to get the midrange drivers. I also used coaxial 3.5" dB Drive mids in the back seat location and added the cap(acitor) from the factory 3.5" to the woofer. This way I have a (almost) true 3-way system with decent imaging for the highs while still using passive 2-way crossovers.
For the front: Use the 6.5" door pods to add a 2-way 6.5/tweeter component setup. Not much room to install x-overs in the doors, so I ran an extra pair of wires through the door loom and mounted them inside the kick panels. Also, I saw recently that there is an eBay seller that is making 6.5" pods for the panel inserts below the rear 1/4 windows. This is likely a better idea than modding the rear factory enclosures, as my idea will only neatly allow for a 5.25" speaker.