They're the category of weapons I've had the biggest fights with, frankly.
Here are my gripes:
1. The twisted polygons used for the smoketrails are surprisingly CPU-intensive, and drag framerate down. Personally, I'd rather have the whole smokepuff thing work like it did in OTA, but with some twists:
A. Desync it, because it's just eyecandy.
B. Don't draw shadows. Another big drain on the ol' GPU.
C. Allow us to specify the texture, or better yet, a texture set.
D. Allow us to specify a smokepuff rate, climb, and decay time, or better yet, allow us to specify a customexplosiongenerator as the smokepuff, so that we can customise it however we want.
In short, instead of a "one size fits all" approach to the whole smoke-trail thing, forcing us to use a variety of not-attractive kludges, give us flexible options. I wouldn't mind the stretched polygon so much if it didn't seem to cause so much lag whether or not it is visible- and, did I note that it draws a shadow whether or not the trail can be seen? Sigh.
2. Wobble needs an additional control: "wobbletime", that determines when the missile wobbles (picks a random vector). Right now, Spring uses a formula for this that is much more complex than it needs to be- it just needs a simple timer. Set the default to 3 seconds, so that the Raven's rockets behave about like they used to, but make it customizable. Short times would make missiles using Wobble act a lot more like GravityAffected projectiles with Accuracy settings >0, whereas setting a very long time might cause errors only on a small percentage of flights.
3. When a missile misses its target, it should become GravityAffected and just drop. The current behavior, where it circles and eventually times out and goes some random direction, is hardly realistic, and eats up valuable CPU/GPU. Not to mention occasionally killing the launching unit

4. When a missile's target dies, the missile should continue on the same vector it was on until WeaponTimer expires, then drop as above. This would make units all firing at the same leading aircraft a LOT more effective, because their shots might actually hit something

In short, I want missiles that:
1. Don't draw shadows beneath them. That's one-liner.
2. Allow for custom smokepuff behavior. Personally, the more I think about it... just let us define a custom explosiongenerator, and that'll get the job done. Really.
3. Don't use the bending polygons. Looking at the code for the missiles... it's really quite cumbersome code.
4. Have non-borked code to handle misses.
That last bit, I'll admit, is hard- how does a missile "know" it missed? Well, I'd like to propose a solution:
1. Allow game designers to assign a "search sphere radius" to each missile.
2. If the missile arrives at the predicted XYZ position of the target, but does not collide with something, then it searches that radius and picks up the nearest enemy.
3. It continues this until it either cannot find a target or the Flighttime ends, whichever comes first. Then it falls to the ground, using the current vector and speed.
Doing the above would lead to far fewer wasted shots, would allow designers to have very dumb (but CPU-sparing) missiles that never found a valid target if they missed, or very smart ones that could retarget over a wide area, wasting the minimum number of shots. If the designer set the value to 0, it'd always just drop if it didn't collide, meaning it would usually drop in the direction of the enemy.
Getting rid of the polygon-twisting code and shadows would speed up these projectiles quite a bit, which I think would more than offset the costs associated with smarter smokepuffs.
At any rate, I can do some of this- some of it's trivial. Designing the search is probably not, but that's the only really hard part, I think.