I rarely pick EE, but even without it, plasma remains quite efficient. (I think I use it at 3/4 range. Further, I just "call" monsters with it).
Maybe you're right about the distance, if you were running and they weren't in your way, but I think you tend to walk back and shoot them at 8 distance, so in that case, rushing into melee seems more time-efficient to me. Commandos are freaking dangerous, but no matter, when running+dodging with HR, Doomguy is stronger :)
And even at long range, one advantage of plasma is that it doesn't knockback, so you'll quickly manage to hit your target
Also, I may value the importance of saving medkits on those dudes more than you (they are tough-enough already without this, ... and I like medkits).
@dropping it
My build are always based on shotguns, but plasma remains cool to quickly get rid of commandos and mancubi. I put my shotty aside when I can get a shambler's head, and the usually associated nano bundled with it, but until the thing is nanomachic, the shotty often remains my main weapon. If I find 2 nuke plasma rifles, I just fill 2 weapon slots with them :)
And having juggler, even with the shell box in prepared, you may switch to your nuke-weapon everytime you're not fighting. Not as comfortable as having it in prep slot, but you could still reload it for 0 time.
About the fact that this pick is good for such challenge... it may, but I still have doubts.
I "stopped" picking HR when trying to get the AoRA/100% badge, and noticed that I spent more time when picking HR than with SOB (I felt sad :( ).
I could probably save more by using less shotty and more chaingun, but considering weapon switches, the 2.5 reload of the chaingun, and more importantly, the fact that it doesn't hit enemies when you run, I still have doubts.
It must be why I love my shotgun, and hate the weakness of this early game "poor man's plasma-gun".
But of course, the use of double shotty when running in melee is great. I discovered only recently that double shotty may have a use (I guess I only tried it as a main weapon before...)
I still see it as a bad weapon (way too situationnal) , but am now concious that it can deliver tremendous damages against a big group, which can be useful in the early.
Yet, I still don't want to spend a whole slot for it, so... I keep not-using it, most of the time, but one-shotting 8 or 9 demons in one single turn is fun
About the other little-or-not mistakes, I guess playing such challenges just requires attention. Fatigue > doomguy :p