Just a few thoughts I've had about various things.
Pounce/Crush/etc...
I don't know if the physics engine is up to this, but I suggest eliminating pounce damage and instead expanding crush to all directions and letting ALL players be capable of doing the adjusted crush damage. Basically, pounce would not be aimable, allowing chomp to be reenabled while pouncing as stacking the damages would require a direct hit already. This would also allow humans to crush at least the smaller aliens, and maybe the larger ones if falling from a sufficient height. To even this out, fall damage would still need to be applied to the human, and probably should be applied to all aliens, although with different damage rates and minimum fall heights. To go with that, the max fall damage cap should be removed. As an example of how this would work, a bsuit falling the three stories on transit onto any alien would just about kill it, although the bsuit would take noticeable damage. In the same situation, a granger would be able to kill a nude human. With this system, the damage would also work going in the other direction. For example, if a rant took a cannon on a map like pushcannon and ran into a human with a jetpack while going up, both would take considerable damage, with the human likely dying instantly, and the rant likely dying on impact with the ground. As a more questionable benefit, such a system would set up well for a flying alien...
To sum it up, crush, pounce, and fall damage would all be combined together into a more generic high speed impact damage which would be applied to both the fast moving person and whatever they run into. Depending on how it is set up, trample might also be includable. Min fall height would probably need replacing with a min speed to take damage. The way pounce would work under the new system is by providing considerable speed to the goon, which would then translate into high speed impact damage to the target.
Jetpack
The only real change that I think should be made to the jetpack is for it to be much more "floaty" with a smooth acceleration to some substantial maximum speed and a much lower air friction value.
Alien Stage 3
I don't really have a way to fix this, but aliens should have at least 2 new classes in each stage. The luci is good enough to be the only new weapon in hs3, but the rant is not really enough by itself. One method to solve this would be pushing the adv goon back to as3, and making adv mara zap be capable of momentarily disabling any targetted human structures.
Basilisk/Adv. Basilisk
The way I see it, the lisk is something like a ninja or assassin. As such, it should be quite stealthy, with no footstep sounds, and maybe a delayed camouflage effect. However, as they seem to be moving to a more indirect support role, maybe at least the adv. lisk should be able to launch a kind of gas bomb that would leave a gas cloud, and cause nearby humans to undergo the gassed effect.
Flamer
It's pretty good as it is, and the usability in vents will be nice. That said, it should probably have a longer range, with the damage being reduced as the distance is increased.
Lucifer
While the luci did need a speed increase, I think doubling it may have been a bit extreme. Something along the lines of 550 charged and 1100 uncharged probably would have been sufficient. Regardless, I think the speed should scale between the two values depending on how charged the shot was. A full 10 ammo charge would go the minimum speed while a mere 2/3 ammo charge would go nearly as fast as an uncharged shot. While this would let mid charged shots reach their target at some noticeable speed, it would let aliens be capable of visibly identifying the more highly charged shots.
Grenade
While these haven't really changed, I do have a few thoughts. There should be a certain built-in variability to the fuse time. They should have a hitbox, something along the lines of a cube with sides of length 4. Granger spit should be capable of defusing grenades. However, as they take damage from other kinds of attacks, the variability in the fuse should be increased considerably, to the point where it might explode immediately or minutes later. In addition, if possible, they should be capable of being knocked around by attacks, like dretch punt.
That's all I can think of now, although I may come back with more.