I do like the levers and knobs on the Proto Throttle.  A very interesting concept indeed.  Alan, I think the way they are using the notches is with a different software programming....meaning moving it up to say notch 2 will play all the correct sound effects, but it also uses software to mimic movement of a typical locomotive with momentum and such.  Similar to what the load setting does on Railpro.  I haven't played with it myself, but that's what it looks like from videos I've seen.
Railpro doesn't fully duplicate notching and brake applications yet.  The load and brake functions are a step in the right direction, but I feel like they need more tweaking....particularly the brake function.  While I like how the load function increases momentum significantly with a heavier train, I would really like a way to control the sound of the prime mover, especially when running light.  Right now with 0% load the prime mover is running at notch 3 while the locomotive coasts down a straight track.  It should be back at idle at the point and the locomotive would just be coasting.
The brake is still a little too primitive.  It works, but doesn't work as smoothly as it should.  Right now you press and hold the brake button and it rather quickly increases to 100%, making it a little unrealistic.  I'd prefer more of a step system, where the braking power increases incrementally.  But how do you do that without a physical lever like the Proto Throttle has?  Regardless, one way or another I'd like to see the braking improved on Railpro.
-Kevin