The Madrid System's main advantages are cost efficiency at scale and simplified ongoing management. A single WIPO application covers multiple countries, a single renewal covers all designations, and you do not need to appoint a local representative in each designated country at the filing stage.
The main disadvantage is the dependency on the "basic mark." For five years after the international registration date, the international registration depends on the home application or registration remaining valid. If the basic mark is cancelled within that period, the international registration is also at risk; a vulnerability that direct national applications do not have.
Direct national applications through local attorneys give more control over each filing, can be better tailored to local requirements, and carry no dependency risk. They are typically preferred for jurisdictions with complex examination standards (the US, for example) or where the Madrid System's rules create complications.
For most businesses registering in five or more countries simultaneously, the Madrid System is more cost-efficient. For one to four countries, or for specific high-value markets, direct applications are often the better route.