1. When compiling the project, if you run into a conflict with features during deployment in Visual Studio while developing the Web template, consider moving different elements, such as lists, site columns, and so forth to different features. Don’t try to put all the elements of the Web template solution in one feature.

2. In Visual Studio, make sure that you turn the Include Assembly in Package option to false. See step 7 of the following article:

How to: Create a Custom Web Template