Flares would be used to call in crates but not just any crates, Trap Crates, crates that would incapacitate a player that opens it, trap crates could release a bear trap(actually, bear traps could be a suggestion all by itself), stun the player(with electricity or a flash), drop an armed mine, or just simply explode upon being opened.
The owner of the trap crate wouldn't know which crate is trapped unless he approaches it, at which point it'll be highlighted red similar to how weapons are highlighted once players are in pickup range(an explanation for this could be that the trapped crate has a serial number on it that the owner will recognise from the flare he/she threw).
And now, for my most controversial suggestion which'll (hopefully) make people flock to this post, flares could also set up an Air Strike(stay with me here...) a flare thrown onto open ground would "mark" that area for an airstrike after which your player would pull out something similar to a C4 detonator, once the detonator is activated a missile would launch into the marked area, instantly gibbing any player caught in it's massive radius and any player caught outside the "gib radius" will just be blown away (both literally and figuratively).
The function of the air-strike would be to restrict a large area of the map to everyone but the owner, which means a cleverly placed airstrike would allow you to play mind-games with your opponent/opponents kinda like "if i go from here he'll airstrike me but if i go from there he'll gun me down".
"But that's OP" you say,(yes, i'm assuming you said that) but you have to realize that the thrown flare will have given every player in the game a giveaway to where your airstrike is set up letting everyone hatch a plan against it or prioritise you as a target.
Then what about closed off maps and areas that don't have open access to the heavens above? Well then, like supply crates an airstrike could just appear out of thin air above the marked area, but if that seems a bit ridiculous, an airstrikeless large explosion could achieve the same result.
Now, for the small suggestions...
instead of incapacitating, a trap crate could drop a jammed gun which would seem normal at first, but will not shoot(and come with a "dry fire" sound to inform players that it isn't just a bug).
the serial number on a trap crate could also be recognised with a sniper from long range, allowing players with snipers to find their trap crate.
If a flare is thrown onto a flammable material, the material will rapidly catch fire.
Flares could instead just be a special ammo for the flaregun, but wouldn't spawn anything unless shot into the air.
a map could be limited to just 2-3 air-strikes depending on how large it is.
I've also thought up of a gamemode where supply crates only spawn from flares, I will elaborate on the spoiler down below...
I also heard that the devs loved worms which is also why I decided to suggest it along with the fact that C4s, as they are now, suck ass (or in other words, are very situational).