Thought I would make an suggestion...Onlink is obviously more complicated than Uplink, in the number of programs, procedures, features, and all of that. Perhaps cheap training programs for hackers can be bought at the Associate that you are provided by Uplink(that small shop with worthless things...make it useful?)

The training programs themselves can be actived, which in turn creates temporary training missions that teach the basic concepts with minimal penalty. This would allow a player to get used to his tools in a unlethal environment. If the training programs are turned off, the training missions are reset and disappear from the map until needed again. The missions themselves do not teach anything, besides being a "sandbox" in which agents experiment.

I think it would be wise for this to be done in a different way.
I shall explain further:

The training would be accessed from the main menu (i.e account logon screen). You click training and choose a mission.
This generates a new "sandbox-style" user, which isn't saved if you log off. Basically, the game is generated without the actual missions and companies, apart from specific ones related to the training mission. Traces result in a disconnection and an email saying "If this were real, you would have been arrested for hacking into <computer name>. Try to be more careful!".

For example, Mission 1 could be "Getting to know Onlink", teaching the real beginners how to run/buy software, access the BBS, read news, look up IPs, stuff like that.
The only real company that would be generated is Uplink, and only the Uplink Internal Services Machine would be there, along with InterNIC.

Mission 2 would be related to a first hack, so the Uplink ISM and a test server would be created.

The other missions would progress through using the other peices of software and doing more complicated hacks.

Obviously, certain missions would automatically give you the software, or a specific amount of cash, allowing you to choose your own.

Seems to be a fairly decent alternative.