I almost always fly in my favorite add on planes, the Realair Beech Duke, Lancair Legacy, Milviz 310, and Airbus X, none of which I believe are native P3D 2.  So I was playing with settings trying to figure out what was bottlenecking FPS, and when I switched to some of the stock aircraft, my FPS nearly doubled , which when you're tooling around complex sceneries, makes a big difference between 18-25 fps and 35-50 fps.  

 

So my questions is first, what are some recomendations for some nice, FPS friendly add on aircraft?  Secondly, is this just a compataibility thing, or do nice add on aircraft just spend that much CPU?

It is both a compatibility and intrinsic issue for addon aircraft. Certainly there are some issues with FSX/FS9 aircraft being optimised for P3Dv2, but also it is naturally more CPU and gpu intensive.

 

Try to avoid glass cockpit aircraft, and anything too complex.

 

I would think something from Alabeo or Ants Airplanes fits the bill.

Take a2a cessna or piper, even digital aviation Cheyenne is very fps friendly, but not so much as the a2a ones

Honestly I don't think their is a difference at the moment between FSX or P3D airplanes other than the installer and whether the developer has added a "check" to make sure you aren't able to cross-install their payware.