You've hit on some points that I wanted to discuss.
Thank you! 
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wouldnt it be easier to just work the controls from a station of computers, rather then having to plug in?
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That's what I wondered, too. I still don't know why they have such an elaborate system for operation in Zion. Why not use mechanical controls? I'd think that they wouldn't trust computers much. It is possible that in order to use ANY computers, they have to tap into the Matrix or some version of it, like the construct. I just didn't think they'd trust computers enough to use them that much.
Re: Neo and the sound barrier... yeah, I was actually surprised that it took him so long to reach Trin, until I realized that it really only took seconds. However long it took for her to fall the distance from floor 65 toward the ground couldn't have been as long as we saw it on screen (thank you slo-mo), but it still seemed to take him too long. In flying to save Morpheus and the Key Maker, he flew 500 miles in about 15 minutes = 2,000 miles per hour! He was already supersonic before he raced to save Trin. I loved the burst of speed evident in the reflection of his sunglasses during that burst, though! Just awesome! :alienooh:
Trin and Morpheus actually did fairly well against the agents. Remember, they are still the same. They run from agents. But they are apparently willing to stay and fight them now, even though they don't expect to stop them the way Neo can. I think their only real hope is to last long enough for someone else to help them out... or until they die.
I'm still working on how Neo stopped the squiddies at the end. There's a theory floating around the internet that the "real" world is actually the real matrix and that what we've been introduced to as the matrix is a program within a program, as if the real matrix is much more complex than what we've been led to believe. If the matrix is more complex, including programs in which individual humans can be allowed enough "freedom" so that they think they're
out of the matrix, then we're in for even more shocks. Neo is an anomolous program, created so humans can have hope. He is human, but he has a greater degree of power within the matrix than other humans... he's also smarter now than his "predacessors" were.
Based on the preview of Revolutions, I don't think there's a greater matrix outside the one we already know, but I think the governing programs of the matrix are losing control. Neo is smarter and has more power than his predacessors; more exile programs are showing up (like the Key Maker, Seraph, Ghost and the Marovingian's other hoards, and even Smith); and the architect seemed surpirsed by the latest incarnation of the "anomoly," Neo, because he caught on quicker and because he personalized his attachment to humanity through Trinity. Personally, I think this last is why humanity will finally win. Neo's personal investment in Trinity will compel him to do everything he can instead of simply doing everything he feels he must. He
won't let her die... we've seen that... and he won't let the world in which he's with her die either. "I can't lose you." Hope is humanity's greatest strength as well as it's greatest weakness.