Same here- I think the Flak Explosions don't really fit; the particle effects look good, but I'd prefer to see how they look like with the 3D model.
3D model...?
Also while I do really like the effect you have for the Fusion Mortar, I'm fairly certain that the Fusion Mortar is intended as a missile and not a primary, that seems like a pretty radical change. 
Well, so, the thing about trails is that it's really goddamn hard to get them to look good. They work in certain cases, but if you try to get them to carry a whole effect it tends not to work -- hence why I tend to use particles more. (I had a hell of a time with that trail on the Shivan primaries, let me tell you.)
Basically, if the trail is really thin, it'll look okay. But anything thick enough that you can actually see the texture, and -- no matter how pretty your bitmap might be* -- it'll come out looking like dull paper. I
think what's happening is that the post-processing doesn't get applied to trails, or something like that. (Because from what I remember, without post-processing,
everything looked like paper.) Maybe they're not considered light-emitting objects the way lasers and particles are, so they don't put off glow?
[*With very limited exceptions. If the trail bitmap is very simple -- just a white core with a colored glow, and a simple gradient, or something like that -- then that can work better.]
I've been toying with the idea of submitting a feature request for the ability to set a trail to render...the way those other things do...but I'd have to learn how to do that, so I'm putting it off.
Also: I'm thinking of making some changes to other missiles; if I do that, the particle effects on secondaries might not be quite so unusual. I don't think they'd work on swarm missiles -- too chaotic; you need the lines to see what's going on -- but things like the Trebuchet I fully intend to turn into glorious particle-trail abominations. (I mean, it
ought to look impressive.)