No predefined systems
No predefined view templates
No predefined filters
No predefined Mechanical & Electrical settings
No predefined dimension settings
No predefined annotation settings, like lines
No standard tags whatsoever
No standard generic families for ducting/pipes/cable trays and routing preferences
No company set DWG export mapping
No set materials, so you'll have to make what you'll need
Basicly you're making a new template alongside a project. This works okay if you've got time on your hands and need to make a company template. It'll help you define the standard which your company uses. However, this is considered more advanced stuff since you're bound to come accross things I've not even mentioned above. But in the end it'll help you understand Revit far better, if you've got the time.
Basicly you'll not run into any "problems" as long as you can find the solutions for them and have the time to apply them.