Possible Story Ideas

[Neoteny]

Remember Neoteny, The Merv didn't have any presence in the real before his acquisition of The General. That's why it was such a big deal back in the day.

He had operatives, didn't he?

If this is a big issue, then Morpheus could always be brought back into the Matrix after discovery of the construct thing ala Beirn and live a program-esque existence, which would create an interesting counter to the program becoming flesh. With the flesh becoming program and all. It would also create an interesting plot point, since you'd have someone trying to destroy the only thing keeping him alive (by Codebombing and trying to take down the Matrix). That's the kind of strong resolve we'd see from him.

Oh, and for what it's worth, I hate the 1999 thing as well. Was a pretty poor explanation.