Attacking a character with high Athletics (or anything else) is pretty simple, as long as you don't simply try to beat it head-on. Simply put: use maneuvers that aren't opposed by Athletics. (Or, ideally, at all.) FATE is highly flexible, and gives you lots of room to work.
There are lots of ways to turn scores in other skills into aspects. Some simple examples:
Alertness: Create scene aspects! Often! See details below.
Craftsmanship: Break the scenery. Improvise weapons from nearby objects. If given time and a distraction, drop the ceiling on him...
Deceit: Distraction and misdirection. Get him somewhere poorly-lit, and then con him into wasting actions attacking looming sacks and crates, while you plan team ambushes.
Intimidation: Use it, maneuver with it, attack with it. See details below.
Might: Can't grapple the opponent? Rearrange the furniture. Overturn crates or bins to create scene aspects, then jump on them for a height advantage. Shove things into (or onto) your opponent. Or just in his way.
Stealth: Get someone to distract him, and hide. Then set up an ambush. Maneuver to give him aspects like "Blissfully unaware" or "He's Behind You!", then tag them for attacks. Athletics is no defence.
If it's "time to fight" the ghoul, why are you letting him pick the battleground? If he's doing something right now that you need to stop, then sure, you'll have to act now. If not... why fight now? Back off, use assessment to create advantages for later use, lure him into a trap, set up all the tags you can in advance.
This is why it's hard to use Investigation/Empathy in combat... you shouldn't need to. A good investigative character should have figured out what he's up against in advance, and used Investigation for assessment rolls (YS p115, p195).
Against a 'typical' ghoul straight out the book, for example... assess his Insatiable Appetite in advance. Then work out distractions involving fresh meat, or taunt him with how hungry he must be getting. Tag it for effect and say he's already hungry and hasn't hunted tonight... if he fails a Discipline roll, and he'll be in trouble.
Just because the guns are out doesn't mean the social rules turn off. Dresden uses, and falls for, social attacks in fight scenes all the time. This is what Intimidation is for.
Example: Defend one character well. Use scene aspects, get him into cover. Then use those weaknesses you assessed in advance... use Provocation to taunt him into attacking, then sit there taking total defence actions. Total defence + "In cover behind the dumpster" aspect is +4 defence, keeping that character safe... while everyone else coordinates on one big attack.
Or just make Threats attacks with Intimidation, for direct social/mental damage. Maybe you can't hit him... but does he know that yet? He can't defend that with Athletics! If you can't take him out with it, even one good hit can hand out a consequence like "Rattled"... which you can then start tagging to aid your physical attacks.
If you tag personality traits that make you want to kill the ghoul, or that are particularly relevant to how you fight, that's a +2 bonus that can't be counter-maneuvered away. Of course, it gets expensive in fate points fast, but that's why you have them.
Use Scholarship or Alertness rolls, Investigation assessments, or relevant aspects, to explain just why you'd happen to have a bottle of holy water with you.
Check the assistance rules (YS p208). Don't all try to hit the ghoul independently... give assistance to your best fighter. Assistance rolls are against a difficulty 1 or 2 points lower (as GM, I'd definitely rule -2 in a situation like this), and every roll made at the lower difficulty is a +2 bonus all invoked at once for the lead. (Adam gets to make his Fists roll... at +4 for "Bea's got my back" and "Charles is keeping him distracted.")
If you couldn't leverage Alertness into combat maneuvers, you were trying the wrong thing. Use it to create scene aspects. Then tag them for help with maneuvers. Check the declaration rules (YS p116); using Alertness to create an against an overwhelming opponent is the default example!
Declare convenient objects to dodge behind. Add laundry that you can drop over the ghoul's head. Confuse it with a sudden turn into a blind alley it hadn't noticed. Then tag all of them for every bonus you can load on.
That's if you couldn't choose the fight location. If you could... you can do much better. Prepare traps. Level the playing field. (Heck, cover the floor in sticky putty. That should be good to restrict everyone's athletics to +2 or +3 max... which'll bother him a lot more than you.)
So far, we have two answers, which appear to contradict each other. I tend to think in practice they're not that far apart from each other, tho.
When you're taken out, you cede control over your fate to the attacker. That means the attacker can assert all sorts of things about what happens to you. Like: you're dead. And because total destruction of the character is on the table, so is any amount of change to the character. Like: you live, with all your consequence slots filled and needing healing. Or: I just knock you out, you'll have a bruise and maybe a headache for the next scene or so — let's call that a mild consequence (or not even that).
(And that's just assuming a physical conflict. In other contexts taken out might be, "And so I utterly change your view of your father. Change the aspect representing your relationship with him on your sheet to reflect the resulting estrangement.")
At any rate, all that nastiness that could befall you (consequences, etc) is still in play after you're taken out. So any notion of saying "sure, I'm taken out" as a way of avoiding consequences is bunk; the only way to avoid consequences for sure is to concede when it's properly time to concede.
So: how much does it matter if the dice hit the table, you take some stress and consequences, and then immediately concede (as has been said) vs giving up and having stuff at least as bad happen to you anyway? Not too much, IMO.
But, anyway, let's look at page 140: It's a summary of the effect, so you can quickly understand what success on an attack means; it's not procedure. There's a page reference to stress and consequences in the sidebar, thereby implying that the official procedure is found elsewhere: page 160.
Doppelgreener's on the mark by taking this text to heart: "If you get hit by an attack, one of two things happen: either you absorb the hit and stay in the fight, or you’re taken out."
As you read on through page 160-162, stress and consequences are referred to as options. Options imply choice. For me, that makes the procedure (essentially): look at value of hit; choose whether or not to take consequences to reduce it; look at post-consequence value; mark off appropriate stress box; if you can't (or won't, tho given that stress is super-ephemeral that'd be a weird line to draw in the sand) mark off the appropriate stress box, you're taken out.
What's being "forced", really, is the handling of the hit, with concession unavailable until after you handle it. Dice are on the table, that hit's coming your way, and you've gotta parse it out with your options or drop, and if you drop, you have no control over what happens to you. Choose to take consequences, and you'll have some control over what's happening to you (including, to a reasonable extent, how those consequences are described); choose not to take consequences and leave yourself with more stress than you can actually take, and you give up all control as you're taken out... including control over whether or not you end up with consequences.
As such, yeah, you could choose not to reduce an incoming hit with consequences (that's the real crux of all of this) and just get taken out by the resulting massive pile of stress. Because it doesn't really matter that you chose not to take those consequences. When you're taken out anything can be done to you: "the person who took you out gets to decide what your loss looks like and what happens to you after the conflict", page 168. I can't see how there's any value in forcing someone to retain control over their character when they don't want it, which is what choosing to be taken out (instead of conceding) is.
Apologies if this seems confused or rambly — it's late!
Best Answer
I tend to think that setting such pairings in stone tends to make the game boring. If Shoot is always opposed by Athletics (or whatever else you pick to replace it), then players justifiably tend to hog those two and all other skills are sidelined.
I believe the best way would be allowing creative use of the whole skill set, even allowing unorthodox choices if supported by interesting aspects. (Remember that aspects are true whether somebody invokes them or not)
Somebody's shooting at you with lasers. How are you going to deal with that?
This makes the game more interesting in my opinion, and no one skill tends to be more important than the other.