The puppeteer

I figured that it was in some way Kusanagi herself. She was the final face, and it later seemed that the Tachikoma had erased the tape of the conversation to protect someone.

It lingers on Kuze too long for it not to be him.

*****SPOILERS*****

Just my thoughts-

Kuze escaped into the Net when the CIA killed him at the end of 2nd Gig. But, being his first time, may be he got scrambled or divided up like a torrent, and floated around separately like he describes:

"Until this moment, I was incarnated across a myriad of egos."

This could be bits of Kuze or the collective subconscious of all the elderly hooked up to the medical machines. But they were not dead, and Kuze's mind was always gripped with a firm resolve to migrate to the Net.

"With this, Solid State is established... and I, the vanishing mediator, now move on to the Society beyond."

The "vanishing mediator"- sounds like the Kuze we know who wanted to help everyone. He just needed some way to collect his parts together and get back in the game.

As Batou says, it could be the elderly, there's no proof. But I think that we and the Major know differently.

Besides, the Major needs to get out of her funk at losing Kuze and get back on the job so we can have the next movie.

It is a cross between the collective concious of the 'Kifu Aged' and Motoko. The puppeteer is one of the cybernetic bodies that Motoko has been controlling. The one that is present at the Ma Sha-Ba assassination goes into the same area and suspension as where it appears at the end of the movie when he and Motoko are interacting. The Puppeteer at the beginning is called a Class A hacker and the only 2 so far in the SAC series to be described as that have been Motoko and The Laughing Man. Don't remember Kuze ever evening hacking in the 2nd GIG. Plus what obligation would the Tachikomas have to protect Kuze by not releasing the last section of the conversation at the end and along with Batou who you can guess also heard the trasmission. Sure it lingers on him but that I feel is kind of a little joke, I was thinking for quite some time before the end that it sounds a little something like Kuze would do. I think that was just to make it all the more suspensful and the real answer more of a shock.

My opinion: A combination of collective concious of the people hooked up to the healthcare monitor system and Motoko's rouge cybernetic body she had controlled in the past that has gone of to evolve into a free thinking being.

I'd have to say it's the Kifu Aged working through the Major. Most of the reasons I have have already been touched on by previous posters, so I won't repeat them.

What I will say is that the Laughing Man and Kuze are kinda out of the running from the get go, as each Stand Alone Complex (as in the phenomena) has a specific goal to achieve. Laughing Man wanted to expose the Murai (sic?) Vaccine's superiority over micro machines and Kuze wanted to start his "revolution."

The Solid State Society's goal was to give a voice to the Kifu Aged about where their assets went (if I recall, I haven't watched it in about a month and a half) when they inevitably died. Motoko's a prime candidate for this goal since, in every iteration of GitS, she has been preoccupied, in some way, with giving "someone" a "voice"; be it 2501, her own ghost, Kuze, or the little girl who needed an organ transplant.