1. Mecklenburg (Charlotte) and Wake County (Raleigh) schools are both experiencing the same issues with overcrowding, etc but Wake County has a better reputation. However there are good schools in both districts. If you choose Charlotte, you could also live in Union County which has a good reputation for schools.
2. Raleigh area is slightly more expensive.
3. Both have a good economy - Raleigh is more focused on high-tech and government jobs and Charlotte is more financial/banking.
Charlotte is and feels like a bigger city while the Raleigh area is more spread out. Besides what you asked, what are you looking for?