Hi Sara
It completely depends on user requirements thus it is quite important to know which KPI (key figures) they need for reporting.
This information will be the base to decide which extractors you need and if you can achieve desired reporting using standard extractors or have to develop custom ones.
When we developed our system the users have basic requirement to see Logistics & Financial data in BW so we started by using standard LO extractors & FI extractors and later upon requirement extended to COPA, Project systems etc.
As you already know R/3 is a transactional system thus it has dependencies to various modules but BW is a reporting system thus in general it doesn't have dependencies like you have it in R/3.
Hope it helps !!
Ashish