To a large extent it depends on what kind of an operation you want to run. There is Single Pilot, Single PIC, Basic Operator and then a full blown 135 operator. Single Pilot is the easiest to get, no company manual or training program required. If you're operating piston equipment it's a lot easier than trying to get turbine equipment going.
Some of the biggest headaches you'll probably run into are the 135 airworthiness conformity inspections on the aircraft. Aircraft maintenance records have to be in picture-perfect shape, and have to stay that way.
The other big thing you'll face on any operation is your Statement of Compliance. You need to go through each and every 135 reg and state how you will comply (if it's applicable).
The process is long, not because it's hard but because you're dealing with the FAA, which by nature, doesn't move very fast at all, especially on initial certification. Be sure to negotiate a Schedule of Events with your Certification Program Manager as a part of the deal. Last time we went through a major change to our operation, we didn't get a Schedule of Events, and it strung the process out to 6 months.
Ray