This basic idea is going to be applied, to an extent, with JAGS--we have a lot of abilities (although generally not so "Basic" as Hero's) and you can apply positive and negative modifiers.
When this is something we can directly test in the simulator, meaning it applies to a combat power (example: Fires every other round after the first) then we can give you an exact decimal modifier that you can use to re-compute the damage per AP. This is slightly complex (most people will want a calculator) but it works, it's balanced, and the list of modifiers, while not tiny, is not huge.
The harder part is where you have some modifier that does not directly impact the mechanical effect of the power. Take, for example, a Force Field that makes a loud noise, sounds a little like a light-saber when you move around with it, and throws off enough electromagnetic radiation that a lot of people can track it (if they have special gear). That's a defect over an invisible force field that you can casually walk around with without cluing people in.
So, okay: it makes the ability worth a little less. Not a lot less: combat (when you really want a Force Field) is noisy anyway. Something that wrecks your stealth is bad if you're a ninja--but this guy probably isn't a ninja. Being trackable isn't fun--but ... ehh ... it's not that bad. We also assume that character designs will generally not be fatalistic: if the character is a wanted fugitive it is not likely they will take an ability that makes them easily found (it is possible--but it is not the "most likely configuration").
So it's worth a little less.
Since we do not do fractional APs, how do we do that? The answer is that we give you Damage Points (called Mod Points) back on each 8 AP of purchase. Let's say that this is an "Inconvenient -2 MP" modification. If you spend 8 AP on Force Field, you get 2 Damage Points back for your loud glowing trackable field.
Let's assume you, the reader, think that kinda works.
What if you spend 4 AP? You get half that--1 Mod Point (which converts to a DP).
What if you spend 1 AP? You run into a minimum MP special rule. You probably get 1 DP but it's a GM call.
Okay. Now let's expand the problem a bit:
I have the noisy force field AND I also have super-noisy glow-y flight. When active I shine brightly, I can be seen coming for miles. I leave "glowing lines of force behind me." Basically it's the same problem: anyone who wants me can find me if I'm using the power. This is also 2 MP. Do I get +4 DP for both of them?
Answer: probably yes. At this point we are still talking about slightly different things--and the glowing-lines-of force are, you know, a little different (the news media can tack you).
So then I get Tracking Sense that lets me scan for people I've "put a trace on" for, let's say, 2 AP--and I do the same thing: it's glow-y? Do I get +1 DP for that?
Answer: AT this point, probably not. See, the collection of Mod Points is based on them having to do something "new" so making all your powers obvious isn't all that new anymore. So probably the GM says "no--that's not new."
Problem 1: This is now a GM call and I'd rather avoid that.
Problem 2: I can make a case that I might use the sense when I'm not flying or using the force field and that is at least theoretically different.
Let's bump it up a bit: What if my Teleport Power creates a "pool of spectral unease" around me that turns people off and makes them mistrust me for a few minutes or an hour after a teleport? That's kind of a defect, right? Then: My mystical armor which is always on does it too. Okay, we already know that it's "no longer new" so the GM could refuse it on those grounds.
Yeah? Not too convoluted.
But wait: having a spectral sense of unease cling to me is kind of a character point Trait. I mean, it's not in the Character Point rules exactly but there are things like Ugly and Obnoxious that kinda do the same thing--they don't get you more DP. They just give you CP.
On the other hand, a "spectral sense of unease" is, almost definitionally, a meta-normal ability (a bad one--but still): it's unnatural. So if it were a good thing (spectral sense of coolness) then it would cost Archetype Points. Right?
So maybe this should get me Archetype Points?
So That's The Problem
There are not just several different categories of defects and enhancements but there are potentially even other currencies that they could be vended in. Superman has two problems with Kryptonite: the first is that he loses almost all of his powers (so all powers have a "Does not work in the presence of Kryptonite" defect on them). Secondly he has a problem with falling unconscious in the presence of Kryptonite. That sounds like an Archetype Point issue: it's very unusual (it's not something normal people can buy--it's related to his unusual / unique physiology).
So What Do I Do?
I think the answer is to simply split things up similarly to the way I have here.
1. If the modification makes the ability less useful (or more useful) it's a Mod Point issue.
2. If it creates the "kind of problem an normal person could have" then you get CP for it.
3. If it creates "the kind of problem a normal person could not have" then you get AP for it.
You are probably limited in how much CP / AP you can get from these.
You might be able to get more than one pay back for a given modifier.
What's an example of #2? Stinky Armor. If your bio-armor has a nasty odor to it then you get a CP Trait the equivalent of Ugly or Obnoxious since the social impact is similar.
If your armor is radioactive, however (minorly, we're sure) you get some AP for it since that's the sort of thing most people cannot get.
In any event, you don't get that much for them.
One More Thing
While I tend to like giving you DP to make up for defects in abilities, if you want to, you can reduce the cost of the ability by 1 AP per 4 Mod Points you have. There's no reason for that not to be legal.
Also Note: there's a limit on how many Mod Points you can get for an ability without GM permission--especially doing things like adding up a bunch of small things. If the idea is that the ability is worth "half as much" because it doesn't work inside 7/11 stores and won't function under the New Moon and doesn't target red-heads, even if you say that adds up to a big defect ... it isn't.
So clearly there will be some judgment calls going on here.