Well, I've become immersed in GE:S ever since the release of beta 4. And while i find almost every aspect makes for a great title, there are a few glaring issues. These aren't all of those that I've noticed, but the most relevant.
It seems GE:S radically altered the mechanics of the throwing knife, either unintentional or otherwise. I've mainly noticed that if you collide with a throwing knife in mid flight, but are not in it's direct projectile path, you merely pause momentarily while the weapon passes. In the original, this would register as a collision and the victim would be dealt damage. Equally relevant was the ability to prepare a knife for flight prior to confrontation by holding the fire button. If this was not done, there would be a slight delay when deploying the knife. GES seems to be lacking this feature, instead firing the knife immediately and bypassing the entire preparation process. This is unfortunate as it gave the throwing knives a unique dynamic which would serve to balance out the increased effectiveness offered by the first alteration. (they're only impossible to use effectively now because of the finicky conditions for a hit)
Equally notable is how the rocket and grenade launcher seem to generate their explosives. Instead of appearing from the muzzle of the gun, they instead, from my observations, appear from the center of the chest. This makes it annoying and occasionally impossible to shoot around corners or over railings where it would seem the weapon has enough clearance. Also in this field was the property of the rocket to adopt your momentum along with it's own when fired. If you were moving left when you launched the rocket, it will continue to move left with you in addition to flying forward. (this also applies to throwing weapons)
And finally, we fall to the issues of moving objects. I can't understand why this isn't more common, but in the original GE doors would have an acceleration value that was applied when the door started moving and when it neared the completely open position. This gave them a feeling of fluidity and realism that the jittery start of source doors lacks. It would definitely be appealing to see in GE:S, if for no other reason than that it was in the original.
Anyway, while all of these issues do seem trivial in comparison to some others pointed out, i nevertheless believe that their resolution would greatly enhance this already wonderful mod.
EDIT: stuck second rocket suggestion in the wrong place. Whoops