Can I mention the weak points of the department I am applying for in my cover letter? I am applying for a faculty position in a small department, which is not very active in research but there is a strategic research. Comparing my previous papers and grants, I can project that I will have a significant contribution to the department to become research active.

Is it appropriate to provide a statistical projection that how the department figures will be changed by hiring me? I mean isn't it impolite to highlight the weak points of the department to justify why they should hire me?
Don't mention anything negative about the department you're applying to. That would serious jeopardize your application.

Instead, emphasize the benefits that hiring you could bring to the department. Do this in a way that pleases the current members of the department.