I like the new fire system, it requires a lot more coordination to deal with them effectively when going against flamer builds.
The thing I would do to change the fire system is allow the chem-spray's buff to be used on cooldown, as right now, preventive fire fighting is an extremely sharp double edged sword during combat.
I was playing as the chem engineer, working with an extinguisher engineer, against a pyra which featured flamethrowers, banshees, and flare guns firing all at one time, which turned out to be a good way to find out just how much fire the new system could handle. The issue I kept running into was that I could keep the buff up while we were out of combat, as using chem on a fully repaired component doesn't activate the cooldown. However, once we started taking damage, then keeping the buffs up would cause the 5 second cooldown, which would mess up the repair circuit as well.
Then there becomes a choice of if you want to use the chem spray, wait the 5 seconds of cooldown, and pray that it can survive those 5 seconds when it's sitting at around 50% health from the start and still taking heavy damage.
Or repair the component you are treating, causing a repair cooldown, giving it more health, watching the stacks of fire continue to grow out of control and possibly missing the chem buff again because it needs to be repaired a second time.
Having watched both components slowly crumble to dust while staring at the chem's cooldown and wishing it away, and watching a single stack of fire grow into 20 after one mallet cooldown, it's a pretty tough decision to make.
Having the buff work outside of the cooldown system, while still requiring the component to be off cooldown to put out fires, would allow the preventive part of fire fighting to still perform in the heat of combat and would require the same coordination with an extinguisher, as chem camping to put out fires would still be very ineffective.
Also, Sammy, that Roasted Duck is just mean.