It includes both versions for the games that are split into multiple versions.
In addition to the games themselves, there are of course some added features, such as an image gallery, a music player, and a high-resolution filter that attempts to smooth the pixels and make them look less boxy. The game also features an online mode where players can NetBattle against each other.
I hope to try out the collection when I get a chance, at which point I will document more details about the added features.