I applied through VFS on December 1 and my friend applied online on December 16. Our visa was issued on the same day.
Sometimes online takes longer than VFS. It depends on the case.
Check the requirements for both online and VFS. There are some minor differences. For Example: Online: You need 4 months statement and through VFS: You need to submit 6 months statement (Visa requirement for Saudi Arabia). Also, if you have credit card than it is easier to pay fees online. However, VFS check your application and let you know if any document is missing or if there is any mistake.