I took out my mp3 player adaptor in my nav charger because the volume level just wasn't loud enough when i plugged in my ipod. well i just got the iphone and I put the rca adaptor back in, and I gotta say, my speakers are much louder!
actually the output on both devices are the same.... you just need to check the following:
1.- Latest firmware on both ipod and iphone (if your iphone is unlocked avoid latest firmware)
2.- Check the volume limit setting on both iphone and ipod and be sure to dissable it, also volume level should be at 60/70 % max...
3.- Disable the option of "sound check" on both
4.- apply the acoustic EQ on both and you'll see a better audio performance on both
hope it helps!