Hi Mohammad,
I would opt for the second option. Bringing all the info into a geodatabase could result in a heavy bloated database. However the questions that you have to ask first are:
The crux is defining the business process business process and the and the corresponding corresponding business requirements business requirements
–– Define the use cases and business processes Define the use cases and business processes
–– Define the user interface requirements Define the user interface requirements
–– Define the data model requirements Define the data model requirements
–– Select technical connector approach based on business Select technical connector approach based on business
processes and requirements processes and requirements
–– Design business logic in conjun Design business logic in conjunction with the requirements and ction with the requirements and
technical connector approach technical connector approach
These old slides (where the above info is extracted) could help: http://downloads.esri.com/support/ProjectCenter/tw_1111_Mark_Causley_PRES_1.pdf