I have this thing about ensemble casts. A lot of my projects feature teams, secret organizations, or groups of people working together for a common goal, and one of my biggest issues as a writer has been "how on earth do I get a number of people to work together without a) overwhelming the reader and b) actually helping people keep all these characters straight?"
Okay, let's do this.
1. Each character has a certain base set of skills.
If you, like me, enjoy RPGs and D&D, this will probably come naturally to you. Think of each of your characters as fitting into a certain class.
Using classes as an underlying way to sort characters is useful-- you can balance out skills more easily. There's the people who can take a lot of physical damage and then the more vulnerable, magical characters. The magician's spells hurt more than physical attacks (often) but magicians cannot take a lot of physical damage. Perhaps it's most easy to see this working in a fantasy setting, but it can be applied to any group of characters.
As an example, there's this one military drama I love that takes place on a submarine. Maybe the people in the command room have some hand-to-hand combat training, but the sub's chief engineer is unlikely to be able to hold her own in a fight, even if she's the smartest person on the boat. Likewise, the ace mecha pilot might be able to accomplish his missions on the ground in record time, but he lacks the strategic foresight to always avoid falling into trouble.
One of the keys to getting the group to work logically together is having them cover each other's weak spots-- figure out ways for them to all balance each other out, with each person being useful. The flirty sniper isn't good at all with hand-to-hand combat, the brilliant strategist captain is actually terrible at fighting of any kind, and the mysterious lieutenant just lives through anything.
2. Ensemble casts are a system of interchangeable parts.
Sometimes it's not necessarily that someone has a certain skill-- a lot of people in the story could have that same skill-- it depends on how good the characters are. Lots of people can drive a car, but maybe there's only one person good enough in your heist story to be the getaway driver.
Likewise, in the submarine drama, it's not hard to find someone can set the submarine's course-- the lieutenant commander can do it, the XO can do it, the captain can do it. But, if the submarine has to evade missiles and be pushed to its operating capability, then the captain (who's designed the sub from scratch and knows it better than anyone) has to be one giving orders.
This also helps you avoid falling into the chosen one trope, if you're not going for that. If a lot of people can fight an enemy but your protag is just trained to be the best at it, or if there are a lot of tacticians but your main character is the most resourceful, then we're more inclined to cheer for them on their merits than on their mysterious powers.
3. Your main conflict is a ripple across character arcs.
Here is a kind of ugly picture that I derped up in mspaint to illustrate this point.
The closer you are to the center conflict, the more I need to see you change/evolve as a character across the story. The people on the outer ring may change a little, but for the most part, they're pretty constant-- they're the most minor of the characters. But on the four inner rings, each character changes in some way (the closer to the center, the larger the change) based on the main conflict.
4. Help your reader remember all these great people.
One of my favorite tricks for helping keep characters straight is associating different letters with them. If all your characters start with the letter J, it will be much harder for a reader to keep them all straight, especially the minor ones.
Granted, if you have a truly huge cast of characters (think Game of Thrones size), then sure, you're going to run through the alphabet very fast. In cases like this, it's probably better to look at family or clan names, and trying to make those unique, then assigning unique letters within them. (Where I'd normally think, "oh that's that T-named character from before!" then I can think "oh that's T-whatever of House S--")
Unique names are cool, but keep in mind what will stand out and what will make your characters blend in. A lot of unusual names together makes more common names stick out (in a sea of Haven's, Pierce's, and Asa's, a Thomas stands out). Likewise, in an expensive preparatory school setting in the US, it's more likely that characters with names like Rohit and Yosuke will stand out and be more memorable than Ashley and Jax. However, if your story is set in Seoul, then a character named Rosalie sticks out more than In Hwa Lee.
5. Quirks win the day.
What defines a character? Sometimes it's just as simple as being the guy who takes himself too seriously and acts snooty, or the specific way that a character opens a door and inexplicably stubs her ballet flat on things. If you can give us something specific, some human detail to associate with a character, something that they do different than anyone else, then we'll remember them more easily.
When Alex Yuschik isn't writing her next YA novel, she's working on someone else's as an intern at Entangled Publishing. She writes about lock picks, ghosts, the abandoned places in cities, and how not to strike bargains with stars. Between sneaking in time to game and rocking out to indie music, Alex spends the rest of her free time working towards her PhD in mathematics. You know, as one does.
You can find her on Twitter @: https://twitter.com/alexyuschik