De acordo com o website GNUpg
GnuPG comes in two flavours: 1.4.11 is the well known and portable standalone version, whereas 2.0.18 is the enhanced and somewhat harder to build version.
As notas de lançamento dizem
1.4.11 is the stable version of GnuPG. (2.0.18 is the unstable development version).
Para 2.0
GnuPG-2 has a different architecture than GnuPG-1 (e.g. 1.4.5) in that it splits up functionality into several modules. However, both versions may be installed alongside without any conflict. In fact, the gpg version from GnuPG-1 is able to make use of the gpg-agent as included in GnuPG-2 and allows for seamless passphrase caching. The advantage of GnuPG-1 is its smaller size and the lack of dependency on other modules at run and build time. We will keep maintaining GnuPG-1 versions because they are very useful for small systems and for server based applications requiring only OpenPGP support.
Se você ler as anotações de cada versão, você criará uma boa imagem de quais recursos estão em 2.x que não estão em 1.x. Por exemplo. suporte para cartões inteligentes.