It should go without saying that, as the game is in active development, everything I'm about to write is only valid as of right now (Alpha 3.22), and can change at any moment; especially with Master Modes, but in the current flight model as well. Also keep in mind that these are my opinions and recommendations based on my experience and play style, and I'm not pretending to know everything, so don't take them as gospel, but they should at least give you a good starting point to experiment with.
The first two things I look at in a ship's loadout are guns and quantum drive. Then, shields and missiles. Power plant in a few rare cases. I don't believe coolers do much, so I don't usually upgrade them.
Guns
For guns, I don't use gimbals in most cases, because I don't like my hardpoints going down one size when I could just try to aim better. They also don't seem all that reliable, though I haven't used them in a while so I could be misremembering. If you like them and they work for you, by all means, use them if you want. After all, hits from smaller guns do more damage than misses from bigger ones.
I do keep gimbals in some cases, to keep the smaller-sized guns' projectile velocity consistent with that of the other pilot guns. The reason you want to avoid mixing projectile velocities is it will likely make you miss shots, as the lead necessary for each velocity will be different. There are currently two projectile velocities: 700 m/s and 1400 m/s. I recommend picking one for your pilot guns and sticking with it (1400 m/s if possible, for a higher chance of applying damage).
Size 1–3
For sizes 1 to 3, laser repeaters are your bread and butter. The reason for repeaters over cannons is their higher fire rate and projectile velocity make it easier to apply damage on fast-moving targets. I tend to use the CF series, because they're widely available, but all laser repeaters are more or less the same (some minor differences in distortion damage resistance, which you don't really need to worry about until you're doing high level PvP, at which point you can look at numbers on Erkul or SPViewer). Except the Yeng'tu, but these you have to get off of a San'tok.yāi. There's also the NDB series neutron repeaters, which are basically laser repeaters, but blue. I use them for aesthetic purposes.
Then, you have distortion repeaters, which deal non-destructive damage, but can temporarily disable guns, components, and even entire ships. If you want distortion weapons in your loadout, a good rule of thumb is to keep it to roughly 25% of your guns. Or you could go full distortion, for piracy and boarding action for instance, or support and defense. It's a good tactical tool to have in your tactical toolbox.
Ballistic gatlings and repeaters are not recommended, because of their low ammo capacity and alpha damage, meaning low full load damage. There might be an argument to be made for ballistic cannons, because of their higher full load damage. Scatterguns I have no experience with.
Size 4
Kind of a wildcard. Pick whatever you want that fits the rest of your loadout.
For ballistic gatlings, the AD4B is preferred over the Revenant because of its much higher ammo capacity. It does come at the cost of higher spread, and so you will have to get close to your target to apply full damage.
Size 5
Avoid laser repeaters, as their fire rate, damage and projectile velocity are low. Go with either laser cannons or the AD5B ballistic gatling. The Deadbolt V ballistic cannon is also solid, but its full load damage is half of that of the AD5B, meaning you'll have to restock twice as often for the same amount of potential damage. The Deadbolt does have a very low spread however—unlike the AD5B, with which you need to be fairly close in order to apply full damage—but then so do laser cannons. Then there's the Absolution distortion scattergun. I've never tried it, but it seems worth exploring. I've been meaning to try a Corsair with full distortion scatterguns, but haven't yet.
Quantum Drive
What I want in a QD is speed, and the ability to go 60 Mkm (ArcCorp–microTech) without refueling.
Size 1
Voyage for ships with small quantum fuel tanks, VK-00 or Spectre for ships with bigger quantum fuel tanks (e.g. F8C, Syulen, Cutter, Defender), Spectre for the Eclipse.
Why Voyage instead of Atlas? It's the fastest size 1 QD that allows you to go 60 Mkm without refueling with ships that have a small quantum fuel tank. More importantly, it's available at Baijini Point, Cousin Crows, and CRU-L4, all of which you are bound to be at or near at some point. The Atlas is slightly more efficient, but not so much that it's worth the trip to HUR-L5 in my view. As for the VK-00 and Spectre, I believe the Spectre is slightly faster between 0 and 38 Mkm, and the VK-00 above 38 Mkm.
Size 2
XL-1. It's the fastest QD overall, and every ship with a size 2 QD should have a quantum fuel tank big enough to be able to go 60 Mkm with it without refueling. If your ship comes stock with a size 2 military QD (Yeager or Crossfield), you don't really need to bother getting an XL-1. But it doesn't hurt either.
Size 3
TS-2. Same as above. For the Reclaimer, I might go for something more efficient, like the Pontes, or a civilian drive.
Shields
If I don't expect combat in a specific ship, I often don't upgrade its shields. If I do expect combat, the FR series is where it's at. Why? High health pool and high distortion resistance.
Size 1: FR-66. Size 2: FR-76. Size 3: FR-86.
Note that size 3 shields are pretty beefy anyway, and the FR-86 is quite expensive, so I don't always upgrade those.
Missiles
It seems that EM missiles are very reliable currently. Too reliable, some might say. I tend to put size 1 EM missiles on ships on which you can change the missile racks. The TaskForce and Pioneer have a large blast radius, and the Pioneer is faster and has a proximity fuse, so I tend to use the Pioneer. The TaskForce does have a much quicker lock time and a wider lock range, so it's a solid choice as well. Smaller size means you can carry more of them, and two smaller-sized missiles do more damage than a single bigger-sized one (e.g. 2 x S1 vs 1 x S2).
Power Plant
No need to upgrade in most cases. To know if you need to upgrade, your ship will probably tell you, and might even fail to take off. You can enter your loadout on Erkul and check the "power" gauge on the right-hand side of the screen. The main ship I can recall needing to upgrade the power plant of is the Hornet Ghost when putting a bunch of energy weapons on it.
With stock power plant:
With upgraded power plant:
For size 1, I go for the JS-300, and for size 2, the JS-400.
Examples of loadouts
Here are a few examples of loadouts I made on Erkul for the purpose of this post.
Note: If you click the "Non stock items to cart" button, then the cart button, it will give you the list of components you will need to buy for this loadout, and where you can buy them (each component will have a drop-down menu with the list of shops that sell it).
Aegis Avenger Titan (ballistic gatling + laser repeaters): https://www.erkul.games/loadout/mWZD3GkW
Aegis Avenger Titan (laser repeaters): https://www.erkul.games/loadout/UCnGiQC9
Aegis Eclipse: https://www.erkul.games/loadout/5I2Fm0tM
Aegis Gladius (laser repeaters): https://www.erkul.games/loadout/OdP0b6nn
Aegis Gladius (laser + distortion repeaters): https://www.erkul.games/loadout/iQacIvEn
Aegis Redeemer: https://www.erkul.games/loadout/7k9UvPUG
Aegis Retaliator: https://www.erkul.games/loadout/YDCsvYEX
Aegis Vanguard series (laser repeaters): https://www.erkul.games/loadout/nEB5VqIE
Aegis Vanguard series (laser + distortion repeaters): https://www.erkul.games/loadout/xjMrnUXS
Aegis Vanguard series (laser cannons): https://www.erkul.games/loadout/KtIyn3An
Aegis Vanguard series (laser + distortion cannons): https://www.erkul.games/loadout/ujIrOti4
Anvil Arrow (laser repeaters): https://www.erkul.games/loadout/7cZ3HxoH
Anvil Arrow (laser + distortion repeaters): https://www.erkul.games/loadout/2XKzgL06
Anvil F7C-S Hornet Ghost (laser repeaters): https://www.erkul.games/loadout/pravVXfV
Anvil F7C-S Hornet Ghost (laser + distortion repeaters): https://www.erkul.games/loadout/WUsq0K7e
Anvil F7C-S Hornet Ghost (distortion repeaters): https://www.erkul.games/loadout/Hmw0S16K
Anvil F8C Lightning (laser repeaters): https://www.erkul.games/loadout/P7lThiEd
Anvil F8C Lightning (laser + distortion repeaters): https://www.erkul.games/loadout/EETDNsZw
Anvil F8C Lightning (distortion repeaters): https://www.erkul.games/loadout/5X1WYXyd
Anvil Hurricane (laser repeaters): https://www.erkul.games/loadout/joi1MhFv
Anvil Hurricane (laser + distortion repeaters): https://www.erkul.games/loadout/ZeLArG6Q
C.O. Mustang Alpha: https://www.erkul.games/loadout/zQaWiu4D
Crusader A1 Spirit: https://www.erkul.games/loadout/7Ri0ehk1
Crusader Hercules series (laser cannons): https://www.erkul.games/loadout/n63JOvLS
Crusader Hercules series (ballistic gatlings): https://www.erkul.games/loadout/ajFhdvFM
Drake Corsair: https://www.erkul.games/loadout/gTZ2NSa7
Drake Cutlass series: https://www.erkul.games/loadout/aKV2jK17
RSI Aurora MR: https://www.erkul.games/loadout/06igQSPN
RSI Scorpius (laser repeaters): https://www.erkul.games/loadout/nz2XSj5C
RSI Scorpius (laser + distortion repeaters): https://www.erkul.games/loadout/eV5l6mTO
