»How did they get Neo?«

In M1, you see Neo being sucked down his "egg" and into a large pool of water, waste, etc. All of a sudden, a giant mechanical arm comes and picks him up and next thing you know, theres Morpheous and the crew. If no ship has ever been within 100 KM of the machine city, how were they able to get him?

Fealds are outside, near the machine city. He is puled out by long tunel, and every tunel leeds in another place, suer. So they located him first, when he was begining to wake up, and prepared in that place.

The pods are actually not near 01....very intentionally.

Remember when Neo and Trin went to the surface...Neo says..."We are over the fields....I can feel them". You can see the towers of pods. There is no fight from the machines at this point. Then they make a right turn to follow the power lines that lead to 01 that Neo saw in his head. The bombs are not sent out until they start to actually approach 01. The pods/fields are not anywhere near 01.

You mut remember that although Zion is a real place, it is under complete control by the machines. This is how they control the 1%. The machines let red pills search for The One in the Matrix, and come to the fields to "free" the potential from their pod. So the Neb simply flies to the surface, goes to the fields and scoops up the redpill they just unplugged.

+ Since there is a 1%, who would want to risk having your capital so near where it would occur anyway?

One wouldn't wnat ot be 'TOO' far away from its main energy source (if indeed that is what the matrice's main purpose is) - large swaths of area to string transmission lines over and thus have to protect/defend would constitute massive energy drains with the more sentrys you have. The distance seems to be substantial as we can't see either the city nor the 'Bomb-shooters' when they make that right turn to follow transmission lines to the city. I'd say we're talking 200 miles away easy.

I'd say that the innards of the Pod structures tie into the existing sewer systems of former human cities. i'm not so sure that the crew has it planned perfectly where Neo is in the Battery structures (thus why they need the trace program) nor where he'll be jettisoned exactly, but they're in the basic vicinity. what makes my skin crawl a bit is if they ever see anyone else they're not retrieving get jettisoned. do they see if they're alive, and if so, are they more than a blubbering psychotically broken mass of living tissue - and worth saving?

Good question. There are other ships patroling the area but if someone is jettisoned that is not the result of Zionite work, without the trace program, the result is most likely...game over. Thanks for playing.

On a side point:
It is interesting how the machine world is laid out, to me at least. The only machines you really see in the pod area are the 'pickers' and the 'pod sitters' - basically your lowly working class machines, whereas the CITY is some 200 miles away and the home of the grandiose looking machines like Deus Ex Machina and the 'hover plat forms' that look like ornate chariots that use the most energy from that area. Hmmm. Seems like they learned something from humans after all.