Sure flying a helicopter and picking up martial arts is reasonably quick, but remember how long he had to sit in the chair just learning basic stuff. And his ability to sit in the chair was far beyond anything morpheus and dozer/tank (always got them mixed up) had seen. Dude was sitting there for six hours or something just learning basic programming and martial arts. There was even a cheap bit of foreshadowing in their amazement: "He's a machine."

PLUS:

Not everyone in Zion has those connectors on their bodies so no, you can't just upload that stuff to everyone. People who can jump in and out of the Matrix are rare because freeing people from the Matrix is rare. Plus the strain on the power supply plus time involved in rotating uploads around so that you don't weaken your defenses is formidable.

Not to mention, the machines have access to the same information and can disseminate it much faster.

So really, not a quick fix at all.