I'll say this as my main reasoning for why flames suck. A flamethrower, launching a full canister of flame juice at an enemy ship usually does nothing beyond annoy the engineers and cause some cussing. Crews spray down hull balloon and engines and then just wait for the Flamer to have to reload and make the guy suffer.
ANY light weapon, by itself, is naught but an annoyance, unless the conditions are just right. If you're looking for a weapon that can overwhelm a chief engineer all by itself, you need a heavy weapon, not a light flamethrower.
It's cool that you're throwing your 2 cents out there. Keep doing that. However I'm simply not seeing the suck from the flamthrower at all. I just spent this afternoon crewing a Flamethrower/Carronade squid piloted by an experienced member of my clan (who plays competitively), and we wrecked the enemy over and over and over again.
Flamethrower/Carronade builds on squids are both quite effective and popular. I crewed one piloted by one of the devs. I myself have a flamethrower/artemis build on mine (which I've used to take down Galleons). I've also seen Flamethrower/Gatling utilized effectively. I've seen double flamer Pyras.
I agree that right now the meta is too restricted to Gat/Flak, and I think Muse is already working on that. We're looking at a new ship, and a new weapon coming out with the next patch. Don't worry, more options for your ships will open up as Muse continues to add content.
Keep flying, and keep getting more experience. One thing you'll learn is that you can win with almost any weapon combo if you and your crew communicate, work together, and performs your roles with competence.