I think people take a very shotgun approach to balance and don't really look at it in a formulaic way.
A general lesson I've learned from a lot of games is that anything which instantly kills you, or is heavily randomized, is not very fun. There's generally nothing that you can do on your own part that would've changed the outcome, so it becomes frustrating.
In regards to damage, there's what I call "Ideal DPS" and this is what a lot of people mistakenly balance around, under the general miconception that the only variables in dealing damage is something like (damage per hit * hits per time unit) vs the hitpoints of the target.
e.g. 10 damage per hit, 1 hit per second = 10 DPS. Against a target with 10 HP, you should kill them in 1 second.
But that's not how it actually works.
You have to HIT. You have to take accuracy into account, and furthermore, when you deal 10 damage in a hit to something with 10 hp, that isn't 1 second of damage, that is instant damage. That is an instant-kill. So in the above example, you can actually have a fight end instantly, or last minutes. This is the oft-ignored portion of damage application: Accuracy and mobility; can you hit them, and can they avoid being hit? This is what actually makes combat systems fun. Nobody cares about playing cookie clicker; it's this accuracy vs mobility thing where individual skill comes into play and everything becomes interesting and challenging.
Another example: In air-to-air dogfights, the challenge/fun is not in spending 3 minutes shooting the ass-end of another plane until it finally falls apart. You spend maybe 2 or 3 seconds shooting another plane, but the previous 2-5 minutes spent maneuvering into/jockeying for that position where you can almost instantly destroy the plane. If you had to maneuver for 3 minutes and then hit them for 3 minutes, it'd be retarded. From a gameplay perspective it wouldn't be fun. You'd never score any kills, or if you did it would be in only the most contrived ways, like - "wow this guy is such a colossal fuckup of gargantuan proportions".
So while instant kills are bad, so too is a Time-To-Kill that is too long.
In relation to Colonial Marines, with Xeno Mutators there was a LOT of that last example, where shooting a xeno only resulted in a kill if the xeno player in question was a colossal fuckup of gargantuan proportions. Thankfully balance has improved since then, but I wanted to offer some advice on how to approach future balancing so that it's more fun for everyone involved.
For example on how I would begin to approach balance - Collecting statistical data for the various weapons in the game - how often does an M41 bullet hit a particular xeno caste vs how many bullets have been fired at that xeno caste (probably this data doesn't even exist), and at what ranges? For example. If your average marine is only hitting 20% of his bullets at 5 tiles, then an argument like, "just hit two burst (of 6 bullets) its easy bro" really breaks down to "Just shoot him 30 times" (and how long does it take to pull the trigger that many times?). The reality is that hitting 6+ bullets on a xeno is not actually easy. They move around, you don't get perfect bursts, and a good hit often requires being at very short ranges. The ticks in byond are inconsistent as well, so you can't assume someone will fire at exactly every allowable tick.
So the reality of Time-To-Kill (TTK) in ss13 is a breakdown of the Bullets-To-Kill (e.g. hitpoints), the speed someone can actually fire that many bullets, and the general accuracy/mobility of the players involved.
TTK = (HP / (Damage * Time Unit * Accuracy%))
Let's take a contrived example: How long can a runner stay alive surrounded by marines, compared to a defender? I think you'll find in most cases that the runner actually lives longer, despite having lower health than the defender does, and this is because the runner is fast and very hard to hit, especially when you risk friendly firing other marines and for a relatively unimportant target.
To finally get to what I've been leading up to:
Damage application needs to be carefully balanced not just in pure mathetmatical DPS vs HP sense, but also with mobility and accuracy taken into account (and at various distances) as well. If you try to balance the game under the assumption that 100% of bullets will hit, you will not end up with TTK values that make sense: If a crusher can take 20 seconds of sustained gunfire from an M41, you can reasonably expect that in actual practice in-game it will take over a minute due to inconsistent ticks, improperly aimed shots, and a crusher that isn't a retard standing still.
I'd like to add that when it comes to instant-kills, it's a good idea where possible to give the would-be-victim some ways to mitigate/avoid the instant kill in a controllable way. I think the best example of this being done well in CM so far is with combat hugging. The recent change that requires marines to be prone hasn't removed the instant-kill factor of combat hugging, but HAS made it more difficult to pull off the instant-kill, and given marines better options to avoid it. In this way there is more of a dance/maneuver which involves some skill on both sides. Whereas previously it was "I clicked you, now you're dead". Similarly, PB shotguns, while frustrating, can still be mitigated by identifying shotgun users and maintaining distance with them - thus there's counterplay. CAS is another example with some counterplay involved.
Examples where there isn't much counterplay at all, are the Tank's LTB and the SADAR, or the Queen's screech and neurospit.