I think that the Nihilanth encounter in the original HL is a bit too simple. Ok, the Nih can teleport you and can launch electrical bolts, but it’s too simple anyway!
The Alien Controller (https://half-life.wikia.com/wiki/Alien_Controller) has a kind of attack the Nih has not: sometimes, the controller opens his head a shoot an orb to you. Why don’t you give the nih a similar attack? In the moment that you crack its head open, it will make an orb that does something (AoE attack? electrical charge? destroy/disable your equipped weapon? shoots randomly in your direction? anything!)
That makes the encounter a little more complicated in the moment it needs something to maintain the climax. What do you think?