The main difference is that Charon cannot mount class 10 guns and has some class 8 harpoints. But it has one turret hardpoint. Nyx is nicer. Charon is more ... public.
Edit: From what I remember when they took my first Nyx from me and gave me Charon, I didn't like the way it moves.
The Charon, is, I don't have any way to describe it. It looks beautiful, performs well in larger fights, but in no way is a 1v1 fighter. I have never had luck with it 1v1.
As per CR request long time ago Charon (Viper MK I) was turned into HF-like ship (turning as slower HF, HF shield, HF guns, HF-like armor, but VHF powerplant), while Nyx (Viper MK I) stayed as average VHF.
Igiss says: Martin, you give them a finger, they bite off your arm.
I have the wierdest urge to make a Junker Charon. Its just SUCH a cool ship, but since everyone says it fails...:(Would it be like good for defending junker convoys or what?