I like the fire-damage idea because it would give another reason to pick Pyromaniac so it isn't just for a "Improved Flamer build".
I think the total cost of thrown "grenade-type" weapons will be re-done after updates so that it requires more AP, but since the damage is bad, I think whatever the new AP use will be, subtract one from that will be a good idea with combination with Pyromaniac.
And yes, I don't think there is any balance between making Flamer Fuel vs Molotovs vs Frag/Plasma Grenades; Frag grenades would always be the best for people that have trouble with HQ gathering.