Mainstream is widely regarded as the more accurate method of measuring CO2 readings. The disadvantage is the sensor, which is prone to being dropped or damaged and is quite expensive to replace. Industry advancements have made the sensor less vulnerable to damage, but the risk still exists.
Sidestream CO2 probably has less potential for major parts replacement because the sensor is internal. The readings may be less accurate because of the variables involved with pulling the sample from the patient to the monitor, then through a water trap, and into the internal sensor. Also, when using anesthetic agents, sidestream monitoring needs to have a scavenge system in place to divert the expired and sampled gas safely back into the anesthesia machine so that the room air during the procedure gets contaminated with expired anesthetic agent.
Both methods are acceptable for measuring CO2. Further research may indicate which method is more advantageous to utilize for your specific procedures and situations. The most important aspect may not be about whether the method is sidestream or mainstream, but that you are monitoring CO2.