What are the differences that take a long time to notice, e.g. Storyline, Secret Servers, etc?

Is there anywhere I can find a complete list of differences?

I send Miah a copy of my long portfolio, if it all goes through I should become the story developer, so in terms of story it'll be different.
Further Onlink enhanced features, and implanted them into Uplink, overal to see the changes and additions, just play Onlink, it'll be a different experience from the core Uplink.