The decision between filing a national application or a regional application involves numerous factors: the number of countries where protection is sought, the filing and translation fees for various countries, and the prior art that may exist in each country. A general rule of thumb is that a regional patent application is more cost-effective if you seek protection in three or more countries in the region.
There are certain countries that will accept PCT applications, but only if you prosecute through the regional patent office (ex. EPO – European Patent Office). These countries include Belgium, France, Cyprus, Monaco, Latvia, Ireland, Greece, Netherlands, Malta, Slovenia, Swaziland and the OAPI countries of Africa. These countries have closed the national stage filing for PCT applicants. However, if you are within the 12-month window after your first (priority) filing, you can do a direct national filing and not use the PCT application in such national patent offices.