First of all, let's establish that I am not currently a competitive player. Let us secondarily establish that I have read through this entire thread, have been playing since the approximate beginning of the thread (perhaps a bit after the hotfix) and have flown with both noobs and experienced crews.
The primary argument against the current state of the flaming damage and counter has not been actually addressed since it was stated. So let's try and keep this short while speaking directly to the topic at hand:
Balance of a specific element or tactic within a game is determined by the relative trouble that one must go to to counter said element or tactic. RTS and certain strategy games are constantly looking at this particular equation when it comes to balance overall and GoI is no different in that regard. Thus:
To counter a specific weapon or weapon combo in GoI one must either develop a piloting tactic to avoid taking damage from said weapon or their crew must be able to manage the damage from said weapon. We will examine what it takes to counter some things and gauge the relative balance based on what is required for that specific combo and how it applies against other possible dangers (i.e, a tactic effective against long range, getting in close and out of arc, being effective against another ship that is also close range). Let's examine a few specific cases in brief. For the sake of understanding, we'll examine guns other than the flamer initially, including combinations, before moving on to the flamer itself.
1. Gat, Mortar. To prevent damage, one stays out of range, one does not get within arc of the guns themselves or one disables the guns before any damage is sustained. To counter damage taken by the guns, an engineer/crew must have a tool or two that can quickly rebuild and repair the hull, probably spanner/mallet.
2. Hwacha. To prevent damage, one stays out of arc (range is less a factor here as Heavy Clip vastly increases the accuracy and range) or one disables the gun before any damage is sustained. To counter the damage, an engineer/crew must have a tool or two that can quickly rebuild and repair the armor/equipment on the ship, probably spanner/mallet.
3. Carronade. To prevent damage, one stays out of range, out of arc or disables the gun before any damage is sustained. To counter the damage, an engineer/crew must have a tool or two that can quickly rebuild and repair the balloon, probably spanner/mallet, and the pilot should either watch their altitude during the initial engagement or be prepared with a tool that can slow the fall while repairs are underway, such as the Drogue Chute.
4. Merc/Hades, Echinda. To prevent damage, one stays out of arc or disables the gun before any damage is sustained. To counter the damage, an engineer/crew must have a tool or two that can quickly rebuild and repair and damaged components, probably spanner/mallet.
5. Flamer. To prevent damage, one stays out of arc, out of range, disables the gun before any damage is sustained or flame stacks applied, an engineer/crew chem sprays all equipment on board within a 25 second rotation or uses heatsink ammo to counter all potential flame stacks. To counter the damage, the crew must have tools which first remove the stacks of flame from any equipment and then repair the damage done/negate further stacks of flame from being accrued. The latter two items are, initially, mutually exclusive from one another.
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Everything has a counter. Everything. The question is for us, as players is, "Can I counter this" and the answer is "Yes". The question for the sake of balance, however is not "Can I counter this" but "To what degree must play be altered for this to be countered". The examples given above demonstrate, quite clearly, that a flamer, a single flamer, takes significantly more work than any other weapon in the game to both prevent and counter the damage from.
Yes, to Janeway, if your crew is 100% immaculate, the ship is coordinated perfectly and your rotations are flawless, you can essentially ignore flame damage. If any one of those pieces is not present, you cannot ignore flame damage and it will become quite frustrating.
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TLDR; Countering the flamer takes a disproportionate amount of preparation, in game coordination and attentiveness to exactitude in comparison to every other weapon/combo present within the game. You cannot expect that level of play from everyone. The problem isn't with the flamer itself, it's with preventative/counter-measures.