I think the problem isn't so much an imbalance in the game (not that i'm saying it's not imbalanced) as a genuine lack of skill/teamwork on both teams.
Now, I'm not an ubercomm, but I've won a couple games in my time, and the first thing I notice (lately) is a complete and total lack of listening to the comm. Usually it ends up with one or two regs doing what they are told, maybe a nub(any non reg) tagging along, and then everyone else wandering around, dying, asking for meds, dying, taking shotguns, dying, OMG KILLED AN RT, dying... And people justify this "but I'm a ninja!" "ninjas win the game!" and then I get voted out of the chair because no one goes to their waypoints.
Marine shooting skill. I watched a euro clan game a week ago, and boy, skulks run from marines like mad. Why? Because marines have GUNS and can kill a skulk in less then a second. I know it's not reasonable to expect leet shooting skills on pubs, but jesus, I've seen single skulks take out 3-4 marines (I've been the marine and the skulk at different times)
And then just a lack of looking/listening at what's going on around them. You know what I mean by this, I bet.
Aliens have similar probles, with single skulks attacking marine start when it's farmed, wandering around blundering into marines and dying, NOT parasiting... 8 minute hive FTW! And.. uh.. totally random chamber placement. Oh, yes, res whoring for onos and dying to LMG marines.
Now, I wouldn't go so far as to call this a problem, more of a.. status quo (and these are simply my observations/frustrations, I'm probably just as guilty as the next guy) the only 'problem' is that a lack of skill hurts marines more then it hurts aliens.