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The P3 is for 3 axles and the P2 for 2. They use the same harness. I would recommend the P3, I had one for years and it is an amazing controller. I would say it is as close to the newer factory Ford unit as you will ever find. The new ones even have memory like the factory Ford ones for different trailers.
Just a quick note on the Tekonsha and harness... if you do go with the Tekonsha controller, they make a direct plug and play harness. It plugs into the truck on one end and the controller on the other. No cutting or splicing. I used one on the 99 I had before I moved to the 06 that has the integrated. It worked great. You can pick one up for $10.
I went with the P2 because I know me, I'd be playing around with all the extra graphics on the P3; I didn't need more distracted driving.
Note: my Tek plug and play harness cost $18 because I needed it now (Camper World price).
I have the Prodigy P2 in my truck. I bought a harness off eBay for like $8, I just had to connect the wiring. As Bryan Ore mentioned- you can buy the one for the controller directly so you can just plug it in. (For like $10-12.)
I had the Prodigy P2 also and it was an excellent brake controller, just upgraded to a 2014 SD and now have the OEM Ford controller. So far it has worked like it's supposed to but I did like the prodigy and the digital readout. It let you know what you were running and whether you needed more was just a turn of the dial.
Rezvani's Latest Post-Apocalytic Monster Is a Ford F-150 Raptor Underneath
Slideshow: Called the Fortress, the 850-horsepower pickup combines Raptor underpinnings with military-inspired features, survival equipment, and a starting price of $285,000.