It could be a collaboration of the two sides of the coin in Freelancer, or even the future. The human brain is a treacherous thing, and I'm unsure if we're completely able to use it on the level of "in-brain-connection". What I assume it is that there could be a chip implanted into or onto the human body, that acts as a human transceiver as a back-up over traditional means. We have a habit of being quite conductive.
As for the neural net, I'm torn in what it is. One part of me thinks that it is a network of computers linked together via organic threads, this is backed up by infocards of optronics in-game; they're much more efficient at transferring data across large distances. They're topographic layout may also take notes from what we understand of the brain, relaying bandwidth like neurons in our heads.
The other part of me agrees with Marburg, that there are chips in our brains, and we can directly access large amounts of information, possibly with HUD or head-pieces designed to translate the data; while our brains relay requests instantaneously, or even through speech recognition. However, I see little incentive over cheaper, and more reliable means with the good old mash the keyboard or holo-board approach.
I'm undecided as to what, but both sides are very possible, at the same time even. It all depends what road was adopted in each place. Different Houses, may call for differing technological approaches. Or widespread adoption of one main technology. Who knows?
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