Personally speaking as a MCH main, I feel like the pre-heated shots animations do contribute a lot to the clunky first impressions of the job, and it does get better at 64. But there's still a lot of clunkiness at max level, mainly tied to overheating.
The first is overheating with Flamethrower. What I've noticed is that the time in which heat starts generating varies greatly, largely due to what I'm guessing is ping. Sometimes heat generation starts instantly, other times it'll eat into the second half of the GCD before it starts. This inconsistency is annoying especially since it's before a WF, where you want to be cutting into overheating time and GCD as little as possible. Another thing, and this is mainly a problem with 2 ammo where you only use one tick to enter WF, is that sometimes the one tick just wouldn't register. After having it happen a few times, I realised it happens when I try to weave in an oGCD, mainly Dismantle, before the 1 tick of FT. So what happens is that the first tick doesn't produce any heat, and you have to wait for the second tick to overheat. This eats greatly into your GCD. Granted, the simple solution is to just not double weave with Flamethrower, but I feel like the option to do it should be available, especially with Dismantle's tight timing.
The other thing is post-overheat. The first is Cooldown not getting the bonus damage despite being cast with OH running. The other is when you return back to the clunky pre-heated shot animations, which creates a really jarring transition from the smooth heated shot animations. The other thing is the fact that Gauss Barrel is still a button. This causes an unnecessary double weave with Barrel Stabiliser, and this also causes huge fuck ups if your ping spikes. Whenever your ping spikes even slightly, the double weave will eat super heavily into your GCD since the game needs to register the Gauss Barrel usage before you can use Stabilizer. The other is that once you use Stabilizer, the game then needs to register that you've hit 50 heat, and will create a situation where you use a non-heated shot despite being at 50 heat, that cancels halfway and you need to press the ability again. This is a ping related issue that can be fixed simply by making Gauss Barrel not a button and instead a trait.