Any double din is a good choice. Buy the wiring harness and the adapter for it since it is a stock 2.2din. You said 6.5 as the top part of the door, its a 5x7 stock. I love my Jensen but they don't make the Jlink anymore and thats the only reason I bought it. Also, you may need to buy a radio adapter, I had to for mine. Though I still never listen to radio. It's just good to have automatic time update.
The mustang also has 5x7 in the rear deck but if done right you can get a 6x9 to fit perfectly, just need self tapping screws (for simplicity). Also the stock 5x7's are very very shitty. Its like have a 4"mid and a .75" tweeter. I have mine laying around somewhere but big difference if you put a 6x8 in the door.
IMO the Din is what your planing on doing. Keeping it stock, then I'd shoot for more Watts/channel.
Planning on adding amps, then I like my 4V HUs. (I've not done any tests on this but IMO, the distance from a HU to a line driver is still able to get added "noise" if the voltage is low. So IMO even if you plan on using a line driver, 4v is better than 2v just like 2v is better than .9v)
Use Ipod like crazy? get one that will cater to that.
Want Navi, then well prepare for more $. I like my phones nav anyway though so instead get an android. GMaps FTW.