I don't remember who said this but "we can't balance the game according to the lowest denominator"
Yes the teams are different...
The aliens with their massive close range damage and high hit points make good lone wolves and often dominate lone humans/ lesser humans( less fighting gear). In public games the excellent players tend to favour the alien side because of it's lone wolf gamestyle and because them playing humans would spoil the fun.
The humans on the other side with ranged weapons and teamwork can dominate the lonely tyrants that can't attack in groups for fear of team damage. example 5 humans fighting without being too cramped in a tunnel where only 1 tyrant fits. Beware a human team that works together.
It is all about playstyle

you said you wanted to reduce the adv goons effectiveness vs turrets well imho the opposite would be nice to see as when you reach stage 3 in less then 10 mins usually it is often very frustrating for an alien player to have to wait outside a well guarded human base( in which the humans sit on turrets and spam unlimited amounts of ammo out) for 40 minutes longer for sudden death to start.
goon at stage 2 would very much kill the game balance as any alien team(against skilled humans) hoping to last until s3 will need to gather as many frags towards s3 as possible before humans hit s2. Grouped stage 2 humans are nigh impossible to kill with s1 or s2 aliens and even s3 aliens can have difficulties.
Machinegun - If you can force a dragoon, adv dragoon or a tyrant to retreat on this then props to ya but I doubt you're gonna finish it off as it retreats with this.
PlasmaChainsaw thingie (I haven't used it so I don't know its name) - Well... Unless you sorta... Throw it...
Shotgun - The spread stuffs it up over distance but then a shotgun wouldn't be a shotgun if you could use it to snipe an opponent down the hallway.
Lasgun - You're still probably not going to be dealing enough damage to take em out.
Plasma Rifle - As I said before, I don't know whether it's just me or if it's supposed to be like this, but the projectiles are really slow.
Chaingun - Great a point blank but I've chased a retreating alien down a corridor and I've seen a large amount of bullets holes everywhere but straight ahead.
Flamer - I admit I can't use a flamer very well... I'm sure I'm torching myself more then I am aliens but then I am comparing the weapons as to effectiveness over a shortish distance while chasing an alien down a corridor and a flamer certainly won't kill it. More like fry yourself.
Lucifer cannon - This seems to me like it's an energy based version of a rocket launcher. Blast radius good for taking out dretches.
1 rifle is meant for the little bugs dretches, basilisk, at a push marauders and for getting money for better weapons/ armour
2 painsaw(or PlasmaChainsaw as you called it) is a melee weapon that does insane damage at short range to *hint*BUILDINGS and bugs
3 shotgun does very good damage at close range- watch skilled players use it
4 lasgun is an affordable base/ dretch/ builder killer for early raids and egghunts
5 pulserifle has among best damage in tremulous (lucifer, flamer and painsaw have better afaik) yes the projectiles are slow so it wouldn't dominate the aliens too badly ( it already does that).
6 chaingun goes good damage with fast moving bullets for killing fleeing bigger bug(goons for example) it is best when used with a battlesuit but watch out for the ammo
7 flamer has very high damage but should be used with restraint when new to the game, it works well when coupled with teammates
8 lucifer cannon should not be under estimated

in the right hands it is the gayest most unbalanced gun in the game ( wrongly used it does suck:) )
you said sudden death isn't fair for humans... do you think a human team that is stuck in their base afraid to kill the dragoons spitting at their turrets deserves to win or draw? humans have equal chances in sd imho. a human that gets steamrolled as soon as sd starts was most likely losing to begin with.
The alien team needs to be able to flee and removing/nerfing the trample and pounce would make it impossible for aliens... also how fun would it be to play humans if you can't even get close to enemy without losing over 50% hp. TIP of the day use the sprint button.
the blaster is meant to be useless... it is a last resort weapon and not an incentive for people to rambo as builder
everything i have said here is probably in the manual if you cared to read it( i never did that is why i typed all this)
I don't care if you tell me my solutions are wrong but if you tell me each side is fair I'm gonna tell you you're an idiot.
feel free to call me an idiot :wink:
@stof making both teams start at s2 would imo make nearly 100% human wins
@seffylight you pretty much got it right
@everyone that read this far sorry for my stupidly long post, what can i say i'm infected