I'm still working on it. I think it's something to do with weird read-only permissions on the cities folder. If I get anywhere I'll let you know.
If you want to manually install and play without the ability to save then...
in the zip file, there's a folder called SC2k, not the first level one, but the one at the same directory level as setup.exe. Copy just this somewhere. I went for C:\games.
Copy and paste the below into notepad. You'll have to change the directories to where you copied the SC2k dir. So it matches up. Also change your mayor name if you care.
Windows Registry Editor Version 5.00
[HKEY_CURRENT_USER\Software\Maxis]
[HKEY_CURRENT_USER\Software\Maxis\SimCity 2000]
[HKEY_CURRENT_USER\Software\Maxis\SimCity 2000\Localize]
"Language"="USA"
[HKEY_CURRENT_USER\Software\Maxis\SimCity 2000\Options]
"Speed"=dword:00000001
"Sound"=dword:00000001
"Music"=dword:00000001
"AutoGoto"=dword:00000001
"AutoBudget"=dword:00000000
"Disasters"=dword:00000001
"AutoSave"=dword:00000000
[HKEY_CURRENT_USER\Software\Maxis\SimCity 2000\Paths]
"Home"="C:\\Games\\SC2K"
"Graphics"="C:\\Games\\SC2K\\Bitmaps"
"Music"="C:\\Games\\SC2K\\Sounds"
"Data"="C:\\Games\\SC2K\\Data"
"Goodies"="C:\\Games\\SC2K\\Goodies"
"Cities"="C:\\Games\\SC2K\\Cities"
"SaveGame"="C:\\Games\\SC2K\\Cities"
"TileSets"="C:\\Games\\SC2K\\ScurkArt"
"Scenarios"="C:\\Games\\SC2K\\Scenario"
[HKEY_CURRENT_USER\Software\Maxis\SimCity 2000\Registration]
"Mayor Name"="flammableBen"
"Company Name"="CarpCorp"
[HKEY_CURRENT_USER\Software\Maxis\SimCity 2000\SCURK]
"CycleColors"=dword:00000001
"GridHeight"=dword:00000002
"GridWidth"=dword:00000002
"ShowClipRegion"=dword:00000000
"ShowDrawGrid"=dword:00000000
"SnapToGrid"=dword:00000000
"Sound"=dword:00000001
[HKEY_CURRENT_USER\Software\Maxis\Maxis\SimCity 2000\Version]
"SimCity 2000"=dword:00000100
"SCURK"=dword:00000100
[HKEY_CURRENT_USER\Software\Maxis\SimCity 2000\Windows]
"Display"="8 1"
"Color Check"=dword:00000000
Save it as anythingyoulike.reg, then double click on it. Accepting all the risk warnings that windows throw at you.
once you've done that you should be able to just run the simcity.exe in wherever you unzipped the SC2k folder.
Simple eh?