Discussion

First of all - to keep this somewhat clear, comments probably should be done through...the comments...at the very bottom.

Items:

CORE doesn't have any but there's quite a few possibilities to implement some. The most interesting approach would be to ignore stats for everything that is basically a tool or other mundane item - notebooks, clothes, lockpicks, etc. If someone's a trained lockpick it'd make sense he has a pick and you don't want to check your equipment bonuses every 2 minutes either. So limiting it is a good idea - preferrably to Weapons, Armor, Vehicles and special gadgets. Weapons and armor are self-explanatory. Vehicles as well - they may have higher stress or be faster or maneuverable, giving bonuses to drive checks in situations where that is important. Gadgets are a little more fuzzy - it could be nightvision goggles (granting bonuses in darkness and drawbacks in bright light) or a camera that works with a motion sensor. It comes down to what makes sense, is balanced, and useful - and also what the player wants. Also, here's a list of basic weapons/armors and how they might work. This would be inherent stats to the different "types" of equipment - ideally, they would additionally still have their individual enhancement bonuses (+1, +2, stress boxes for armor, etc):

Weapons
Ranged:

One option with ranged weapons: An option to deal with clips would be to give any character the option to, as a standard action without a roll, require another character to do a (free) guns roll to see if they still have ammunition left. Not sure about the opposition - could be set by the GM based on how many rounds they have been using the gun, could go against the opponents Alertness skill. If they tie or fail, they have to spend an action to reload their gun before they can continue firing.

Handguns: +1 to deceive rolls to conceal the weapon. Gain a +1 to defend against Martial attacks.

Aspects: Small, Flexible

Revolver: Gain a +2 to a single roll with this weapon during a conflict. Reload before firing again.

Aspects: Small, Reliable, Limited Clipsize

Shotguns: +1 to targets in the same zone, -1 to targets one zone away.

Aspects: Large, Slow

Automatic Handguns (SMGs, Automatic Pistols) +2 to rolls for covering fire

Aspects: Small, Limited Clipsize

Automatic Rfiles (Assault Rifles, Machine guns):  +2 to rolls for covering fire

Aspects: Large, Automatic

Sniper Rifles:  -1 to targets in the same zone, +1 to targets one zone away. Aspect:

Aspects: Large, Slow, Armor Piercing

Explosive (RPGs, Grenade Launchers): Inflicts 1 stress on a tie.

Aspects: Bulky, Inaccurate

Fire (Flamethrower, Molotov): ???

Aspects: Burning

Thrown (Knives, Rocks, Hatchets): Can use Martial to attack with a -1 penalty.

Aspects: Small, Silent

Arrow (Crossbow, Compound Bow): Count as melee for the purposes of armor defense property.

Aspects: Large, Silent, Piercing

Beam (Laser, Plasma): Inflicts 1 extra stress through burning on a shift 2 or higher.

Aspects: Unreliable, Ammoless

Electric (Taser): Ignores armor. -1 to rolls.

Aspects: Nonlethal

Melee:

Small (Knives, Hatchets): Can be used as ranged weapons

Aspects: Small, Silent

Blade (Sword, Axe): If you defend against an attack using this weapon and succeed with style, inflict 1 stress on your attacker.

Aspects: Large, Slashing

Blunt (Club, Staff): When using full defense with this weapon, gain a +3 instead of a +2.

Aspects: Large, Crushing

Pointed (Spear, Halberd): Can attack enemies in an adjacent zone.

Aspects: Large, Piercing

Unarmed (Fists): +1 to attack rolls on unarmored targets.

Aspects: Attached, Silent, Crushing

Electric (Shock Baton): Ignores armor. -1 to rolls.

Aspects: Nonlethal

Armor
(note: Because the way ranged defense works, the +X bonus of armor designed for ranged defense cancels itself out with the penalty to athletics. Bonus - Penalty = Net Gain. Since Martial can be used to defend against melee attacks, it's not necessary for those armors)

Kevlar: +2 ranged defense, -1 to athletics

Aspects: Restrictive

Multi-Threat Vest: +3 ranged defense, +1 melee defense, -2 to athletics

Aspects: Restrictive

Reflective Armor: +3 ranged defense against beam weapons, +1 defense against other ranged weapons, -1 to athletics

Aspects: Restrictive

Metal Plate Armor: +2 ranged defense, +2 melee defense, -2 to athletics

Aspects: Bulky

Active Camouflage: +1 to Stealth rolls when standing still

Aspects: Unreliable

General
Two things. First - I got the idea about compelling wrong. You take a -2 (or rather, someone else gets a +2 to their defense roll or a pasive defense) by having your aspect invoked against you (by another character), which gives you the fate point. Compels are different - they are not roll penalties but basically an automatic failure - see page 14 for an example, and page 71f for more explanation of how this may work. In short, a compel is a narration of why a character fails at something he attempts.

Second thing - keeping track of fate points in roll20. The solution - use a card deck (top right, second button from the right). Just edit the existing one by making the number of cards infinite and changing the backing (very bottom of the edit window) into something more appropriate, like a poker chip for example, or a coin (should be a png for the transparency). Then you can just deal fate points, everyone sees what the others have at all times (including the players seeing the NPC's points), and they can drag them out and give them to someone else (usually the GM).

Location Stunts
Totally an option with fate - just create stunts for a specific location. For example: If it's dark, everyone gets a +1 to defenses against attacks from another zone. If it's an open field, you can move an extra zone in turn for taking a -1 penalty on your action roll. If there's a bad mood in the air, every social roll to exploit negative emotions gains a +1. And so on. Not a necessity, but an option.

Altered
A few things about the altered...first of all: The "normal" ones going batshit and shooting up the city isn't something that could conceivably happen often imho. If it was anything but a rare occurrence, the altered would be rounded up and/or killed. Having a specific group of people act out occasionally will breed hostility and discrimination, having a group of people regularly go on murdering rampages will lead to actions to contain that risk factor. By locking them up and/or killing them all, especially in a society that isn't democratic. Which would suck balls for players.

Secondly, procreation - the "gene" or trait should be recessive. Why? It's simple.

a) If the Altered in the wildnerness would have children that aren't Altered or crazy, they would probably kill them

b) If the Altered in the city would have children that are Altered, that would mean that, on average, the percentage of Altered in the cities would about double each generation (presuming that every single person has two children with someone else). First 5%, then 10%, then 20%, then 40%...there's some other factors that would slow it down as the number grows, but the point is within a couple of hundred years there wouldn't be any regular humans left unless there were very drastic measures.

So the proposition would be to to make bein Altered recessive. That way, if two Altered in the wilderness have a child it will always be Altered as well. If an Altered has a child with a Normal in the City, the child won't be - unless the mother is a carrier, in which case there's a 50% chance. Which is why the government may try to enforce mandatory scans before allowing procreation to control that.

Lastly, the brain scan thing, I can see a problem with that: From the sounds of it (genetic test is not sufficient, lots of indicators that may or may not give it away) it's supposed to be not super easy to figure out. If that wasn't the intent and it is supposed to be super easy to figure out, ignore the rest of this paragraph. Anyhow, the thing about the method is - a DNA test, like a paternity test, takes more than a couple of days. A complete brain scan can take anywhere from 1/2 to 3 seconds depending on how advanced your stuff is, and considering that it's very conceivable that within 100 years of technological advancement, we're far enough to just point a device at someone, have it scan their brain and analyze the results (and you don't need to be a medical professional to recognize one specific mutation). So, if the intent was to make them harder to detect, brain scans won't work.

Oh by the way lastly, different degrees and power classifications, I've already suggested those. Yay or nay?

Money Stress Track
So I was reading the Strands of Fate rules for some Ideas on weapons and armor and I happened upon the wealth stress track (p. 242). It's probably too complex to worry about now but something to keep in mind if we introduce enhancement bonuses for weapons and other more powerful mechanics for items. A very simplified version would be: Every player gains another stress track for wealth. If they try to buy an item, they roll their resources against the cost (set by the GM) of the item. Any shift below the price is added to their wealth stress and remains there. Shifts above the price are ignored. Selling the items works in a similar way - the player rolls their resources and gains their shifts above the price -1 as a bonus they can spend on future purchases. Negative shifts are ignored, but the item is gone. If a player fails a buy roll by more than his stress can soak, he receives a special medium consequence and cannot buy further items until it is cleared.