Fate has a much more narrative approach, less GM authority, and player-based plot control mechanisms. This can make for trouble transitioning from a more adversarial GMing environment.

Fate Core (and other recent Fate games such as Dresden) actually do a pretty good job of providing a suggested "menu" of powers and stunts for players to take; show them to your players and let those inform other stunt ideas through play, rather than trying to get the characters completely nailed down in advance the way you would have to in D&D.

To address the specific problems you mentioned:

• The "blind sniper" problem is that in Fate, it's very easy for a cooperative party to stack multiple temporary aspect bonuses on a situation, then tag them all for a single super-successful roll regardless of innate skill.

  Consider a sniper with a base skill of +0 - "has no idea what he's doing". First he hides on high ground (creating aspect "On a Grassy Knoll"). One of the other players - a tech - has made, and gives him some "Precision Armour Piercing Ammo", with suitable aspect. Then another player jumps into the road to stall the target into "Standing Still for a minute", so the sniper can create advantage by taking an acting to put him "Centred In My Sights".

  Then the sniper free-tags all of those, for a base roll of +8 and a near-certain hit - with fate points to spare if he needs them.

  Stacking enough of this sort of this can greatly reduce plausibility, but it's obvious behaviour for a group of D&D players where it's an expected part of the system to need to stack every combat advantage you can generate. I don't, however, feel it's as much of a problem as some Fate players do - this is behaves-as-designed. Fate characters are supposed to be able to beat pretty much any single obstacle if they can generate a convincing narrative. "He's not that good a shot, but it worked because an entire team was helping him take it" is a pretty good narrative to me, and gives the plot and characters room to develop further.

• The "constant compels" problem arises when GM and players get caught in a Fate-point loop of constantly compelling aspects to force behaviour or non-actions from each other.

  Remind your players, and remember as GM, that the point of compels is to implement narrative development. The Fate point economy will naturally limit how far players can push this, so it's not a problem unless the GM gets sucked into constantly offering Fate for compels. So don't. Compel when it's a narrative or character development to do so, not just because it's possible.

• Long combats occur because groups have trouble actually taking out opponents of similar skill levels. This is particularly likely if your group is used to D&D, and trying to "wear them out" by all attacking individually. In Fate it's much more effective to set up a narrative about a couple of major attacks, taking multiple actions to support each other and make those go off well.

The best counter to most of these issues is threefold:

1. Let them have their moment. Players being able to tear through obstacles like this is not a problem in Fate the way it would be in D&D; it's expected behaviour of the system. Don't make it impossible, but ask what happens next and generate new obstacles. The problem can come more from a D&D-oriented GM feeling he has to make tasks "possible to fail" than from actual issues.

2. Your enemies are not idle. Don't GM in direct opposition to the player's actions, but instead change the game. Fate uses the same mechanics for social and combat conflicts, and it does so for good reason, expecting them to intermingle. Use it. Enemies will attack on social fronts, run away if they're in trouble, consult allies, adjust schemes, and all the other narrative options that are not often available to an orc in a dungeon.

3. Remember that in Fate, the player is always an informed participant, even when the character isn't. The gap between player and character knowledge is much bigger in Fate.

   Situation: A hostage is tied to a chair. There is a trap which incinerates the room if anyone touches the hostage.

   D&D answer: Tell the players nothing. Make hidden Perception checks. If anyone explicitly searches, make Search checks. Lie unless the players succeed at these checks.

   Fate answer: Tell the players immediately that there's a trap. Let them make rolls and use aspects freely to see if the characters spot it. If one of the players has a "reckless" or "rescuer" aspect, compel it - offering a fate point if their character runs in carelessly and sets the trap off. Make the players partners in decisions that hurt their characters.

Fate Worlds: Kriegszeppelin Valkyrie

You might find what you want in Fate Worlds Vol.1, specifically "Kriegszeppelin Valkyrie" (KV). It is a mod/campaign where PCs are WWI pilots. Their planes are stationed on a giant flying aircraft carrier, the eponym Kriegszeppelin Valkyrie. Change "planes" to fighters and "flying aircraft carrier" to "capital ship", and you have a good start!

Now, that's probably not enough detail for you, so let's mention some rule points and how they might fit what you would like to do. I will avoid quoting extensively considering the book is not open source, but here it is.

Fighters

Fighters are represented by Stunts. Each fighter costs a given amount of Refresh (between 0 and 3) and gives specific bonuses. One fighter would for example cost 2 Refresh and grant a +2 to Pilot rolls to defend and create an advantage due to high maneuvrability. Another would cost 1 Refresh and grant Weapon: 2 once per combat due to heavy guns.

As for damage, the combination Pilot+Fighter symply uses the pilot's stress tracks as is. You could however create a separate "Piloting stress track", with additional stress boxes for higher Pilot skills.

Dogfights

Dogfights in "Kriegszeppelin Valkyrie" are handled through a simple rule. Fighters making a straight attack without first placing an advantage on their target can do no more than one stress damage, no matter their Stunts, their roll, their final result, and so on. A fighter needs to first succesfully create an advantage on their target to be able to do full damage.

Capital ships

The Valkyrie in "Kriegszeppelin Valkyrie" is treated as its own character. It has its own stress track, Aspects, Trouble, Stunts, and skills. It uses its captain's skills and stress tracks for mental attacks.

This makes sense, considering a ship with a huge crew is less dependent on its pilot's skill. Put Han Solo at the helm of a capital ship, and it probably won't be much nimbler despite his superior skills.

Other ships

"Kriegszeppelin Valkyrie" has a couple of other ships described as opponents:

• Gunship: Heavy guns and bombs
• Troopship: Transport carrier
• AA Gun: Anti-aircraft gun
• Airship: A big flying ship, but smaller than the Valkyrie.

Fate System Toolkit: Scale

You mentioned it already, but for the sake of completeness I would like to point out the Scale subsystem in the Toolkit which might help you reach what you want.

You define a number of scale steps (3 or 4). Larger entities have a number of bonuses against smaller ones. This allows you to split ships into size categories (fighters, freighters, small capital ships, big capital ships). The more categories you have, the more difficult it becomes for small ships to affect bigger ships, which might or might not fit what you have in mind.

You could change the bonuses to be more similar to Star Wars RCR: for every step separating two ships, the smaller one has bonuses to attack and defense, but the larger one has bonuses to damage and armor.