Is Neo the only "One" to have an opposite like Smith? If so, why? How was Smith able to do the things he did (copying himself unto others, flight, etc.)? Why could no one else do what Smith did?

Yes. As Smith put it at the start of Reloaded "It's happening exactly as before...Well not exactly." As to why well that comes from understanding how which is never fully explained. Smith sudgest that it was apart of Neo copied onto his code mixed with his inablity to accept that Neo had killed him which then lead to his exile.

There really isn't much to go off of but if I had to make a guess it would be that Neo was the first to ever really kill an Agent by terminateing the code within them. Not just beat them till they had to find a new host but to send one back to the source and for Smith this was something that he couldn't believe happend. to quote Smith

"I killed you, Mister Anderson, I watched you die... With a certain satisfaction, I might add, and then something happened. Something that I knew was impossible, but it happened anyway. You destroyed me, Mister Anderson. Afterward, I knew the rules, I understood what I was supposed to do but I didn't. I couldn't. I was compelled to stay, compelled to disobey."

I suppose any other program could have done what Smith did; if they were so inclined.

In part 1, Smith described humans as a virus. Between the beginning of 1 and the end of 3, there was a progression of Smith becoming more human and Neo becoming more machine. Smith's morph into a virus was ironic considering his hatred for humans.

I always attributed his power to copy/overwrite to AI. AI created better AI; that escalation.

I also always had an underlying thought that Smith worked for/with the Merovingian. How else did he escape deletion? Perhaps Frenchie hooked Smith up with an 'upgrade' which enabled him to copy/overwrite.

This theory isn't supported when Smith says that he "wants Everything!" but it makes more sense to me now that Merv is poking around a lot more into the Real, somewhere we know Smith was venturing. He got into Zion and was on his way to 01.

As for opposites, I think Neo is the only One to have an opposite. The cycle apparently worked the first 5 times. But this time it didn't. Smith was supposed to be the balance to the equation. So does that mean the Architect endowed Smith with his copy abilities? If so, it contradicts my Smith/Merv hypothesis and it also means that the Architect and Dues Ex Machina have a communication problem. But I don't think they do. That would be inefficient.

I suppose any other program could have done what Smith did; if they were so inclined.

In part 1, Smith described humans as a virus. Between the beginning of 1 and the end of 3, there was a progression of Smith becoming more human and Neo becoming more machine. Smith's morph into a virus was ironic considering his hatred for humans.

I always attributed his power to copy/overwrite to AI. AI created better AI; that escalation.

I also always had an underlying thought that Smith worked for/with the Merovingian. How else did he escape deletion? Perhaps Frenchie hooked Smith up with an 'upgrade' which enabled him to copy/overwrite.

This theory isn't supported when Smith says that he "wants Everything!" but it makes more sense to me now that Merv is poking around a lot more into the Real, somewhere we know Smith was venturing. He got into Zion and was on his way to 01.

As for opposites, I think Neo is the only One to have an opposite. The cycle apparently worked the first 5 times. But this time it didn't. Smith was supposed to be the balance to the equation. So does that mean the Architect endowed Smith with his copy abilities? If so, it contradicts my Smith/Merv hypothesis and it also means that the Architect and Dues Ex Machina have a communication problem. But I don't think they do. That would be inefficient.

Hmm, that is a very interesting theory, and one I have never thought of. But, one thing I noticed while watching the films is that The Merovingian never once speaks of Smith and visa versa, right? In fact, not many characters acknowledge Smith's existence except for during the Burly Brawl, when he runs into Neo, Morpheus, and the Keymaker in the Hallways, and when he fights Neo and Trinity as Bane. It's a little ironic considering the fact that he ended up consuming everyone in the Matrix. So, I don't think the Merovingian assisted Smith, but I'm not sure how he did escaped deletion. Maybe sheer will power? Another question I have is: Was the Merovingian absorbed by Smith, or did he escape in a construct or something?

Yeah, they never speak of each other. But with such a complex storyline I feel like I have to answer questions the movies left me with. Perhaps they purposefully left things open ended for the audience to decide. I know Pulp Fiction did that.

As for Smith's method of escaping; your guess is as good as mine. The other agent he overwrote knew of him, but he didn't really seem to be after him. I assume agents would track down exile programs.

And the Merovingian; I would guess a construct, too. Though they don't reveal all his methods in the movies, we now know he can get anywhere via the Effectuator. I highly doubt he'd hang out in Mobile Ave while the machines reload the matrix.