Why was bane the only one copied over?Because he(smith)should of copied over mostly all the redpills by part 3
Because the "red pills" had almost all evacuated The Matrix at this time, because Commander Lock insisted all hovercraft be back at Zion to defend against the attacking squiddies. It was a struggle to get permission for one or two ships to go back up and allow access to The Matrix.
But, as we see, Morpheus' crew and Niobe's ship were there at the end of Reloaded. Smith tries to assimilate Morpheus (and Neo) when they are rescuing the Key Maker, but he doesn't quite get to them. The Key Maker knows too many secret doorways.
Hopefully you noticed in Revolutions, that by the end, Smith HAD assimilated all the billions of blue pills living in the Matrix, not to mention The Oracle, Seraph and Sati.
Also why did smith's copy die after bane died?
Because he didn't have a body to live in. In the Matrix, Smith only needs to be a program. But in the real world, the Smith program needs a computer (or human brain) to operate within. When Bane's brain died, so did the Smith copy within it.
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