One big problem they have is being the ambush enemy type. There's not even a sound cue or a unique audio for them, no way to know one's in the area until you've already encountered it or played things before. It exists almost entirely to be a "Gotcha!" moment (no, not to Doom II) on your first playthrough and a UN run ender, because there's only like three of the damn things in the campaign, and if you can catch it before it hits you it dies just as easily as any regular Prowler. It's one thing to be surprise-slapped by a teleporting jerk without even seeing him first, it's another when their slaps turn your legs into jello and require a strong slap back after they already teleported away.
Maybe you can't just remove them now that they're here, but if they never existed in the first place they wouldn't really leave some gaping hole in TAG2's pacing or design.