Strong enemies are Arachnotrons, Mancubi, Hell Knights and Barons. Plasma Gun is for either taking out single strong enemies or large amounts of light/medium enemies. I can't say for Brutal Doom since I avoid it like a plague, but here's how I usually use the guns. It's up to the map designer to limit your access to the better weapons that use a specific ammo type, then ramp up the difficulty once you get them. In general, in most situations, the BFG is 'better' than the plasmagun - but this is no different than the chaingun being better than the pistol, or the SSG being better than the shotgun. If you're fast enough, they'll have very little time to react.) (There can also be another whole layer of gameplay in multiplayer because the 'traces' are fired just after the projectile hits something - so you can fire it, time your shot, then duck out from behind a wall to hit someone. To efficiently kill a single enemy like a Cybie you've got to get in close, which can be tricky - especially depending on the map design. The BFG's actual damage calculation is weird (if you think the projectile itself does anywhere near all the BFG's damage, you need to read this) and it's spread out in front of you, which makes it best against crowds and swarms. AFAIK (And I kinda suck at doom but I know some things) the plasmagun has two main benefits: It's precise (the most accurate weapon in the game) so it's amazing for picking shit off at range, and it has the highest rate of fire of any weapon which makes it the best choice if you need to stunlock an Arch-vile or Cybie.

Doom 3 plasma rifle