From what I understand (from reading the wiki entry for a few minutes) is that the antenna converts the waves into electrical currents, which then has to be converted to a usable signal by a detector sub-system (no idea what that is...). Maybe a bone with conductive properties wold serve as an antenna, but the neurotransmitter would receive gibberish unless it could modulate the current. Perhaps microwaves or some other form of electromagnetic radiation could serve as a from of wireless transmission.

Maybe whatever device lets the brain control the body is protected by an EMP shield?

Then actors would be (significantly) more expensive. Plus, you wouldn't be able to fit it within the cranial cavity with everything else jammed in there...

EETS THE FYOOTURE! Miniturization works wonders.

The entire process is this: Transmitter receives signal from signal processor (encoding from usable signal into more efficient signal to be broadcast), emits in the form of some sort of electromagnetic radiation (long waves are more efficient in atmosphere, so radar or radio), receiver is placed within range and sight of the signal, waves excite atoms in the antenna which creates an electrical signal of the same oscillation, decoded by the signal processor into a usable form and goes to whatever is waiting for the signal.
I don't see how that can't be made entirely organic, with copper or iron making up an antenna and nerves doing the decoding.

No technology today could really be used for these kind of things, it's either never explained or it's a future format.

And anyways it's going to stay like it is, making an emp that instakills everything is boring and makes the game not fun.

Even if there is an organic receiver, the EMP would temporarily scramble radio (and virtually any other signal known to man) resulting in a massive seizure. Depending on how reliant bodies are on the remote signals, they may even suffer cardiac and respiratory arrest. So yes, EMP's would affect meat bags.

instead of killing meatbags, maybe paralyze them for a little bit?

A sufficiently powerful EMP will already mess up human brains.
With a faraday cage, the robot's and craft's controllers could be made immune.
The very skin of the robot would probably protect it from a large portion of the emp's waves, though for real protection there could be no gaps wider than a few cm. Either way, they are better off than the poor coalition clone who just got his nerves fried in a horribly painful blast.
As for an organic radio communication device, we can already accidentally pick up FM on properly tuned braces. That's nothing like the bandwidth needed for this sort of thing, but in CC's future we're growing hundreds of clones, building advanced androids, and playing with ridiculous energy weapons.

I think the emp should not kill anything, it would be too hard for you to decide what's shielded and what's not.
Instead, temporarily blocking the human controller from using them would be great (Though useless against the CPU).
This way they would still have their independent systems and on-board AI, but no communication would reach them,

You could do this in a variety of ways, but my experiments with changing an actor's team have been crashing.
Permanently setting them to an allied but uncontrollable team would probably be the most desired solution.
A more laggy solution would be to assign all mechanical actors to a list, then cycle that list for a period of time, checking to see if each is controlled, then returning the controller to his currently assigned brain.
Or something like that.

Actor:GetController().InputMode = 3

Fuel air bomb
Very cool!

Another good option would be all in just one download for those who want the entire contents

Added the cluster bomb and the fire bomb. And bomber.

In a fancy package, too. Just like you asked.

for the napalm bomb thingy, try adding the emitters similar to the disruptor grenade in the dummy faction.

I need more ideas, I suck at them

Here's a really cool tip:

MAKE AIRSTRIKES.

Like the ones in Duh's pack of stuff. Except less generic.