So one of my players and I got to talking about how you might design an ability where the FP cost were variable depending on how well you rolled to activate it. This got me to thinking – how the heck could I do something like this? I eventually came up with a conclusion that wasn’t uber clunky and thought I’d share.
To do what is needed you’ll want the following three modifiers:
- Reduced Fatigue Cost (+20%/level) (p. B108)
- Limited by Margin (varies) (Pyramid #3/9: Space Opera, p. 16)
- Optionally, Costs Fatigue and/or Requires (Attribute) Roll for traits that lack those two things (p. B111 and GURPS Powers, p. 112)
Now, with a bit of mathamagic you just combine these modifiers in a workable way to get the result you wish. First, if the ability doesn’t have a activation roll and it’s meant to be an active ability add Requires (Attribute) Roll. If it doesn’t require FP to use add whatever level of desired amount you wish with Costs Fatigue – I wouldn’t go over 10. Next, add Reduced Fatigue Cost modified by whatever level of Limited by Margin you wish. Do note that this can increase the cost of abilities that do note natively require FP.
A few examples:
Burning Innate Attack 4d (Costs Fatigue, 2 FP, -10%; Reduced Fatigue Cost 2 (Limited by Margin, Full-power at 2+, -10%), +36%) 
Healing (Reduced Fatigue Cost 10 (Limited by Margin, Full-power at 10+, -50%), +100%) 
Picking Over the Bones
The idea is sound, but due to some oddness with Costs Fatigue you can get an ability that is worth more character points than not having it. I think one way may be to simply treat “Reduced Fatigue Cost” as worth +5% when combined with “Costs Fatigue.” That seems sooooo much fairer to me. In that case, that innate attack might look like this:
Burning Innate Attack 4d (Costs Fatigue, 2 FP, -10%; Reduced Fatigue Cost 2 (Limited by Margin, Full-power at 2+, -10%), +9%) 
I think that is much fairer in price even though it amounts to what is effectively a feature for the ability.
What do you think? Silly? Stupid? Did I go to far? Not far enough?
I really like the idea of FP variable cost based on a roll. It mimics some fantasy settings, for example in Naruto the "energy" cost of a power is based on your control over the "ki technique"
Saying that, I really think that in this case is much fairer to say that "Doesn't cost fatigue" in this context is priced at +5%
An additional idea, for a "Spells as powers" approach:
Let's suppose we want to make a roll to "cast" and a roll to "hit" (as in traditional magic spells). The roll to cast is used only to calculate the fatigue cost. If you fail the roll to cast you really cast the power, but you have to pay the full cost.
Burning Innate Attack 4d (cost fatigue 2 FP -10%, *Variable Fatigue 2 +8%) 
*Variable Fatigue 2 is: Doesn't Cost Fatigue 2 [+10%] with (Based on Attribute Roll -10%, Limited by Margin 2 -10%) [+8%]
I like this approach for the Chi Sorcery 🙂 Chi Sorcery is exhausting for the novice, but affordable for the master.
Instead of "Cost Fatigue" you could use "Cost Corruption" to make a dark power. If you pass your will roll for the required margin, you don't have corruption, but if you fail … well the dark powers allows you to cast the "spell" but you have corrupted your soul. This approach is not good for an Horror Campaign, but it could be good for a DF one.
I like all of this. I must put more thought into this. Hmmm.
Re: The Costs Fatigue/Reduced Fatigue Cost discrepancy;
When something doesn't have a fatigue cost and you have Costs Fatigue, you aren't using Reduced Fatigue Cost to then erase it. Like with cyberwear, you are negating a disadvantage (er, limitation) rather than adding an advantage (enhancement). Therefore it should be No Costs Fatigue (which as you intuited, would be +5%/level).
Yeah, I really need to revisit this at some point to see what else I can puzzle out.
Could you not limit the limitation, which while optional is at least in the books.
IE costs fatigue (reduced by margin) -~4%/level
You can't limit a limitation. You can limit an *enhancement* per p. B110. Lots of folks use it as a house rule, but I'm pretty sure it's not RAW.