The downside of agent-based replication is the management and cost overheads involved in keeping the agents up-to-date. Conversely, agentless replication, by its very nature, avoids these overheads providing a much cheaper solution. However, it also requires systems to be offline while backup is taking place, which for critical systems is often unacceptable.
Businesses need to weigh up the added cost of agent-based replication against its benefits in order to decide whether having systems offline is acceptable. In general, if a system is business-critical, it should use agent-based replication. For non-critical or remote systems, short offline periods are no great problem, and agentless replication should be used.