Either agent is acceptable. CO2 will be less expensive as the cost of this fire extinguishing agent is far less than FM-200 (technically defined as HFC-227ea by NFPA 2001). Both agents will exclude oxygen from the space when they activate (FM-200 also interrupts combustion free radicals) so the room egress systems needs to provide for the design occupant loads and have well engineered pre-discharge alarms. Employee training on the required actions to take when a pre-discharge alarm is activated is equally important.
Under NFPA 2001 the integrity of the enclosure (e.g., Room) requires a "tightness" test as a condition of acceptance and annual tests upon system acceptance. This is required to ensure that the room or space has very limited penetrations or no penetrations. This is done because of the agent cost. FM200 systems are not required to be discharge tested because of the room integrity test.
For CO2 systems, a full discharge test is required. A room integrity test is not required because NFPA 12 establishes minimum leakage rates. However, minimum clearances from energized electrical equipment must be satisfied due because a discharge of liquid CO2 can create a static discharge. See Annex A of NFPA 12.
Depending on the volume of the enclosure, a CO2 system can consume a large amount of space, especially if high-pressure CO2 cylinders are used. FM-200 system will require less space since the agent is more effective at controlling an incipient fire.
You haven't asked anything about the detection systems so I am assuming you have resolved the method for activation of the fire protection system.