GodBen, I completely agree with your assessment of this episode.
One of these days we're going to disagree on an episode, and then I'm going to feel bad.
"If the radiance of a thousand suns
were to burst into the sky,
that would be like
the splendour of the Mighty One—
I am become Death, the shatterer of Worlds."
There is a good scene in this episode where Neelix and Jetrel are talking about what happened in the aftermath of the Metreon Cascade and Jetrel explains that he would never be able to apologise for building the weapon so he never tried. I love James Sloyan, he also played Admiral Jarok in TNG's The Defector
which is my favourite episode of that series. There's some great acting going on there and you really get the sense that this is a man haunted by what he has created. So the Oppenheimer quote came to mind (I play a lot of Civilization 4), and that led to me learning that he took it from sacred Hindu scripture. So I learned something new today.
I liked the episode very much, but there are problems with it. I shall now list them so as to prevent myself from making a very muddled paragraph.
1) While this is a very good use of the Neelix character, he is still annoying in some scenes.
2) Neelix/Kes doesn't work. It just doesn't, stop trying.
3) The dream sequence irritated me. It didn't add anything that we didn't already know and it looked goofy.
4) The idea that Neelix is blaming Jetrel for his own cowardice is silly and a cliché. The guy built a weapon that killed your family Neelix, I'm pretty sure that you are angry at him and not yourself.
5) We really didn't need Jetrel trying to deceive everybody into saving the colonists. It felt tacked on and distracted from the emotional character story they had been telling.
A good episode, some annoyances, some structural problems but ultimately it is the kind of show I enjoy.