KEGG FTP vs KEGG API
I found the way to download the genes and pathways thanks to this answer using KEGGREST. 

It seems that the API allows to fully download the database because it allows to download info, list, find, get, conv, link, ddi.

In fact in the message of 2011-05-21 it mentions that the API includes more options to download the KGML files that previously where only possible to get via the FTP site.