As far as adjustments to enemies go, I feel that the alien grunts inflict a bit too much damage with their hivehands, considering the homing shots and rapid fire capabilities. Just one of them can cut down the player’s health significantly, and in Xen we’ll be facing far more of them. The Icthyosaur seems too weak and underused. Perhaps twice as much health, requiring 4 or 5 crossbow bolts to bring down, and generally place a few more of them. Leeches could appear as a particle effect like the roaches instead of being an actual foe, making the watery areas more interesting. Or at the very least place a tank of them in one of the labs in Questionable Ethics. A zombie marine would be a welcome addition later in the game, perhaps first appearing in On a Rail or Surface Tension. And maybe my aim just isn’t very good, but the Xen Masters seem very tough for skinny flying things with giant heads.
As for specific level design, my biggest petty gripe is with the ending to Forget About Freeman. This is the last time we face the marines, and the final battle with them is usually won by the aliens for you, followed by a couple sentry turrets. Building on suggestions by others, might I propose a final confrontation with five or six marines instead of those turrets? When you approach this seemingly empty corridor, suddenly several troops jump up and start firing, like they were waiting for you. And if the player chooses to retreat, it would put that giant maintenance bay to good combat use.
In We’ve Got Hostiles, some of the scientist placements don’t make sense. There are three locations that would almost require the marines to have walked past and completely ignored them. Two of these are when the player approaches, only to see them immediately run out into the open and be gunned down. Why would they do that, at that exact moment? The third is when two of them are trapped between turrets and laser mines. How did they get there? And yes, I know these are moments from the original game, but they made no sense then either.
Last is the epic battle on the cliffs with the helicopter. It is way too resistant to the RPG, as many others have stated. My suggestion is weakening the chopper to explode when hit with 2 or 3 rockets, but to compensate the player must down a series of three choppers before proceeding along the cliffs. And maybe encounter one or two more later in the chapter.
As for Xen, I agree with others here that there is no real clear objective, just roaming around hoping to stumble upon the Nihilanth by chance. Perhaps some vortigaunts, away from the eyes of their masters, could point you in the right direction. Maybe a scientist of two, stranded on Xen but having managed to survive, could provide some exposition. Also, only found in Xen: zombies wearing HEV suits!
Looking forward to seeing what the development team has done to expand upon the Xen chapters!