It appears that the skills learned via the uploading process actually show up in Neo's brain, as in the sequels he fights using Kung-fu outside the Matrix.
Muscle memory/reflexes are stored in the nervous system. If you are uploading data to one cluster of nerves (the brain), doing so to the spine (and other nerves) as well hardly seems unreasonable. So even the reflexes should show up.
The physical condition of the people stuck in the matrix is atrophied, but the process by which they fix the bodies of people who leave the matrix seems to duplicate their physiology inside and outside the matrix.
In the Matrix, Neo (and the other free humans) also cheat (to a greater extent sometimes than others), and for the most part that ability to cheat (pre-blind Neo, if you think they ever got out of a Matrix) won't be available outside the Matrix.