I just passed a little session of beta testing the new version during the last hours, here's the result:
Sometimes, when I look at my map, there are blue colored server which doesn't have any reason to be colored (no missions affected to 'em). This thing could be solved if, instead of having the game deciding which server should be blue colored and which shouldn't, you add a "Colored" option to this little button allowing to add or remove a dot from the map. Some kind of "Not visible/Visible and colored/Visible and white". This thing would also help when you're connecting on a mainframe or a LAN and need to bounce on a server from the same company just before etablishing the connection since, even if the mission server are colored, the public access server aren't.
Revelation and all its different version shouldn't be available in the start-up feature.

Nice feature, but to tell the truth, it's not really useful on most program. This thing should be only available for the security system (Motion sensor and Gateway nuke), several special program, like Revelation Tracer (or is it tracker? well, the one which show the server infected by revelation), useful when you wan't to make a backup or your game before attempting the Arunmor's final mission, and a similar option which open the program when you just connected on a server (mentionned several posts ago). It would allow you to start the proxy/firewall/monitor disable or bypass, and the trace tracker program just as you connect on a server. Sadly, this one wouldn't be cool at all when you're visiting Public Access Server, or Uplink Internal Service System, and it require you to code something so it only does this on Mainframes, LANs, internal service systems (Excluding Uplink's one), and Government server (excluding InterNIC).
Similar to the point above and easier program to code would be a Trace Tracker v5.0 which automaticly launch when connected, or a Voice Analyser v2.0 which launch automaticly when calling someone.
Also, I don't know if this bug was also present in the original Uplink, make some research if you wan't to know if it's only present in Simply Uplink, but, when you start a new game, there are already news about server which got rebooted or suffered from a major data loss in the Uplink's news section, but IF you receive a "Destroy this software" or "Elite agent required for system destruction" mission, no matter if it's stored on a LAN or not, and IF the company you got to attack were already in the news at the begining of the game, then you can already tell your employer you accomplished your mission, and you'll get the "mission completed" email and money from your employer.
Nice job you did on the search, it run smooth and fast now, keep up the good work.