Notable gameplay related changes from original:
* Energy leeches were removed
* Rails no longer electrocute
* Rocket test chamber tentacles can't be sneaked around when they're smashing on the same floor simply because of too wildly random swiveling (that is: distractions are much more mandatory)
* On the rails no longer has player changing where the rails lead
* Gauss gun ricochets off the walls instead of penetrating them
* Scientists no longer heal Freeman
* Alien grunts are no longer immune to weapons fire at armored parts of their body

Other notable changes:
* Certain level segments have been omitted or streamlined, making levels shorter.
* Certain level segments have been made to make actual sense (or at least some, unlike the complete lack of seen in the original)
* Weapons are received in different order and in somewhat different places than in the original