This is sort of general, and not type specific:
Autobrakes typically give you a given deceleration rate, and are activated shortly after touchdown.
The pro is that you get braking immideately and evenly; this is ideal on short/slippery/contaminated runways or if a specific turnoff needs to be made, or in strong crosswinds.
The con is in absorbed brake energy and thus heat - if you have a short turnaround time, heavy aircraft and limitations in use of reverse thrust (or any combination) you could very well run into a brake cooling issue.
With manual brakes, the pilot can modulate the brake pressure manually with the foot brakes, from zero to max pressure. It also allows a delayed brake application, which reduces brake heat issues.
The type of materials used in the brake units may also be of interest. On carbon brakes, wear is primarily dependent upon the number of applications rather than the force and duration of the application. The even and continous nature of autobrake may be useful here if use of wheel brakes is anticipated all the way to taxi speed and brake heat is not an issue.
Steel brakes wear primarily based on duration and force of application, so a delayed brake application (ie manual brakes) may reduce maintenance cost.
Furthermore, the economical aspect of the brake wear may vary from operator to operator. The other primary means of slowing the aircraft after landing, reverse thrust, costs fuel and engine wear. Depending on the maintenance cost structure of the brakes vs. engines (think warranty/no warranty or variable price vs fixed price for overhaul), and cost of fuel, may influence the Standard Operating Procedure regarding use of wheel brakes vs use of reverse thrust.
For any given landing, the pilots will, with due regard to safety, comfort and economy, based on their company SOPs, determine which setting will give the overall best result. (And yes...this much thought actually goes into this decision for each and every landing...but of course it gets easier with time.)