Sorry I was typing that response too quickly and didn't proofread enough. It was pretty vague.
What I meant was: Fast Missile Racks in the current build generates 15% of the base flux of the ship per use (not including capacitors, concentrated shields, etc). I have changed that in the next build to only generate 10% base flux per use, a 33% reduction in its cost. It keeps its small cooldown between uses (10 secs) and now only has 2 charges. Charges will take significantly longer to regenerate than the cd (every 100 secs I think).
The charge-based ship system is quickly becoming a necessary theme. 
Heh, true enough. I think that sounds reasonable.
Wasn't it a x cost per missile slotted before? Or am I recalling that wrongly?
Trying to make sure I completely understand what you mean or would like to see: So you think Harpoons cost too much flux? Or they cost too much flux when used with Fast Missile Racks? Or is it more the issue that I will respond to below, as well, regarding misleading tooltip info?
The second mainly. Using them with Fast Missile racks. Hence the changes should help with them, Reapers, and so on.
Most missiles cost a lot more flux, and there are not a lot of "Assault" variants. (As in, low-no flux cost) Mainly there are those PD missiles. Which excluding assault mostly makes sense, It is hard to find a reasonable missile to use.
Also, just so I have a frame of reference for your experience, is this mostly through equipping them on condors, or have you also tried them out on any higher tech ships, if you have them? I can understand what you mean about the condor's lack of flux if you are equipping advanced missiles like the Harpoon or Hunter. Because of its nature as a conversion warship from a freighter, I tried to somewhat limit its combat capabilities in accordance with lore. It's cheaper, and easier to maintain and deploy compared to full combat destroyers, and provides decent fighter support without sacrificing every last drop of combat ability like the Anchorage does- the other low tech destroyer-sized carrier in this category.
Ah yes. In vanilla, it is far easier to use all the slots without horrible flux costs. The problem is that there aren't many missiles which aren't flux hungry, and ships like the Condor and Crucible, and honestly most missile-heavy ships tend to have to either use Reapers, anti-fighter missiles, or suffer massive flux costs. There aren't many lighter-weight missiles around. Will try the smaller racks though.
Fast Missile Racks being present is also misleading when outfitting the condor for the AIs use. Since that system will likely be entirely wasted- even in the next build, if you are using advanced missiles that generate more flux than the condor can handle. So you are right in this case that builds for this carrier will likely revolve around: Do I lean more on its combat ability (luddic church, hegemony and pirates typically take this route) or do I give it some heavy-duty fighters, bombers or gunships and use fast missile racks for things like swarmers, trebuchets, bolas and salamanders. Combining the ship system with lighter costing missiles or a combination of heavy flux missiles like the trebuchet and flux free ones like the salamander can really let you see the system shine even on the condor.
Yea, it has too few reasonable builds, and it's ability really doesn't fit it since it still doesn't have enough flux to run it all, or even close.
Maybe that ship needs a little more in its description to let players know its missile limitations. Your thoughts? Any counter arguments?
**Edit: Also, the Harpoon(single) or Sabot(single) version works a lot better on the condor with its system, and saves some ordinance points as well.
I agree that tooltips describing "flux per shot/salvo/burst" are needed. Unfortunately, unless things have changed since I last checked, the U.I is off limits to mods. Otherwise I would add both of those entries below "flux per second."
If it has indeed changed, an API file path to the file that handles the weapon tooltips would be very helpful in this case.
On your suggestion: By tooltip do you mean the description in the tooltip? That, I can edit at least. I can try and add that information, but it will kind of look weird and out of place. Guess its better than not having it though, and so likely necessary, especially considering ships just wont be able to use certain weapons, like you said. Still, it will take a little time to get all that information into the descriptions. There are quite a few weapons that fall into that category. 
I know you can't touch the built-in tooltip, something I asked for as a suggestion a while ago. Would be really useful for a lot of modders.
I mean the description, like how you did for fighters. (Something that got lost from vanilla when they became weapons and you couldn't read it's stats anymore)
Just something like: 2,000 Flux/shot, and 2,000 Flux/sec for 3 seconds would do it. It says 60 shots a second peak, and you got 3 ammo? Easy to calculate by brain.
That just says 2k minimum flux storage, and 6k or 8k to unload all the missiles.
I wonder... Can you hack the cooldown on those missiles, such that after firing it sets the cooldown to 1 second? Or for, like, any strike type weapon?
I mean, being able to unleash 3 missiles in seconds which do terrible, terrible damage is one of the perks of a Harpoon, and even with the flux cost that is the purpose. Just that 450 flux is not quite 6k flux.
The big problem though, is that I looked at the missile, saw 150 flux/second, and said, Yes, I can equip that. I have 200 or so flux dissipation, so it will be a bit tight, but no issue. However, once I try to actually use it, the serious flux impulse shows that is not really the case.
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Concentrated Shield Emmiter's tooltip says it reduces shield damage taken by 25. you forgot the % there.