Not really complicated, at this moment they are interchangeable - although there are some important differences.
Mondero was the first RFID transportation payment card and has been around for a few years (more than 3 is all I know). It was released and is managed by a private company and was originally meant for use at the subway as well as kiosks, theatres, etc. This card contains no personal information - just the balance of the card.
SUBE was introduced by the government about 2 years ago in response to the change crisis. It is an electric card just like in any other city that atually is linked to your DNI, so if you lose the card, you can get the balance back. Originally CFK had said it would be implemented 2 years ago, and now they are just in the final steps of implementing it on trains and the few remaining buses. This card is the same technology as the Monedero, it just goes through a different (govt. owned) processing center. The only physical differences is the placement of the RFID chip within the card.
SUBE in my understanding is not available for foreigners without DNI. Monedero in turn is easy to use & works the same - without requiring a DNI.
You can pickup a SUBE at any Correo Argentino and Monederos are available at Centros de Atencion for the subway.