marines do more damage, have more health, and have the advantage of being ranged. they can upgrade to weapons easily capable of one shotting most aliens, even the onos doesnt stand a chance against an exosuit despite costing more. the only thing you can do is try to sneak up on them, but most of the map is lit up by default, and even in melee range an assault rifle will do more damage than a skulks bite will. it's not like you have the benefit of numbers either.
It's not nearly as one-sided as you make it out to be. Hell, for a while, the Kharaa were considered to be the OP side. Sure, in a stand-up fight in a long hallway with no cover, Marines will win every time. But how many maps are set up like that? Many rooms have high ceilings, multiple entrances through the ventilation ducts, and so on.
The strength of the alien side is that they have many tricks and abilities to negate the marines' "advantages". They can turn invisible, move much faster than marines can, and have very disruptive attacks and abilities (bile bomb, spores, etc.). A good alien team will force the marines to split their attention between multiple points on the map, as well.
If you're really convinced that aliens are inferior, try watching some competitive games on TwitchTV or Youtube.
Skulks are ambushers, in fact all of the aliens are ambushers, even the Onos.
Aliens are fast, but they aren't durable enough to use that speed in battle to overwhelm the marines. Aliens have to use the speed to run away and retreat so they can flank the marines, attempt another ambush in a different location, or cause havoc in an undefended base.