User controls are easier to create in comparison to custom controls, however user controls can be less convenient to use in advanced scenarios.
User controls have limited support for consumers who use a visual design tool whereas custom controls have full visual design tool support for consumers.
A separate copy of the user control is required in each application that uses it whereas only a single copy of the custom control is required, in the global assembly cache, which makes maintenance easier.
A user control cannot be added to the Toolbox in Visual Studio whereas custom controls can be added to the Toolbox in Visual Studio.
User controls are good for static layout whereas custom controls are good for dynamic layout.