I agree with you on the spoon thing, it was a different spoon, and the kid he saw in the matrix could have very well have been in zion and wanted neo to remember the beginning of his 'voyage'. Smith always seemed to know exactly what was going on, and where he could meet neo, which further shows the connection, and he also seemed to be setting him up, if you listen to some of the comments, as kaizix pointed out, you would have seen this.