For the original question, I think most modules are fine. However, there are a few...
Flak simply feels weak. Mostly because single-target DPS is so low, even with multipliers. You need both 4 targets and multipliers to match the equivalent basic weapon module. In general, for an AOE module, I'd rather have a Lightning Turret module (or Electric Shuttle, if you prefer).
Acid are OK damage wise, but aside from polycrystal, those multipliers make them rather niche.
Paralyzers tend to focus fire too much. Otherwise, they do very good DPS and paralyze. Outside of the nebulas, these are a very good general choice.
Rail Cannons have odd multipliers. A cross between the three basic types? They seem to lack purpose overall.
Finally, the drones. Two problems there.
First, I think the drones have too short a lifespan. Especially the Slicer drones, which spend most of their lifespan chasing down the enemy before they can even attack.
Second, drones do not inherit targetting orders from the main ship. That means it is impossible to get any kind of focus fire with a drone-based Champion (with microing every drone every 2 seconds).
*cut*
Most of the normal modules I have a bit different problem with. They come with many shots which leads to very spread out damage. And they don't seem to respect focus fire in any way so you end up with them scratching paint and main gun actually killing things. At least until you have really many of them.
When I right click a target, all modules (in range) fire on it. If you have a save where they're not doing that please send it my way.
Hmmm..
What you write works for me once. It works only for target you click directly. I'm not even sure if target has lots of health if it works longer than few seconds (didn't test that on a golem). After that.. it's free land each module shoots whatever it wants. They do keep targeting priority.. mostly.
In attached save champion is next to barracks. Pop them and target one of maws. First maw will die with everything shooting at it. After that main gun and modules start shooting other maws - but modules spread fire as they want between them. And with not enough maws for all shots modules shoot other targets. Thats best visible with MRLS I think since it has many shots.
Net effect is that modules prefer maximum spread fire (like paralyzers should). I have paralyzers on this champion so you can take a look how they target. For me after maws (can't paralyze but they respect target priority) they would focus fire (like other modules should with focus fire on?). Looks like logic is a bit.. other way around 
Right clicking each maw in range one after the other (need similar thing with hybrids but there preferred target fails while it holds here) is kind of annoying. And for maws for example you really want them dead like.. yesterday. I would expect similar thing with other high hp/high nastiness targets.
In a related item, I've got a save here were the champion is only attacking with the main gun (despite having a full load of other weapons).
I don't have a save for it at the moment, but I've also seen the 'modules attacking things other than ordered' effect, a lot. I'll post a save if I can get one reliably duplicating.
