Android apps will get no more permissions then what is coded in the app by the dev and accepted by user at time of installation. There is no difference in permissions for user and system apps. System apps come installed so you don't have any choice.
Note that these permissions pertain to android specific permissions like internet connectivity etc. Unix su permissions are different and both user and system apps can request superuser privileges.
So the bottom line is no difference in functionality. Only one diff system apps will survive factory reset.
My Android Apps
- Android Play Store Link
- Think Sparks
My Dev devices - MDPI
- Tablet Karbonn ST8, HDPI
- HTC Desire with JB 4.1, XXHDPI
- Nexus 5 Stock