|Databases Contain Empty Holes!|
The size of Windows Installer databases is a major reason why people don't use it (although most people are thinking of InstallShield generated "MSI"). With the tiny overhead with tools like NSIS its hard to convince them.
The fact is if you try to reduce the size of your MSI by dropping large tables etc the size of you MSI can increase by 60K. There is no API to remove these (potentially huge) "empty holes" and there is no tool or even manual mechanism available which can remove them (without danger or creating a non working MSI).
Also see "Databases Are Not Compressed!".