I am just wondering what is the differences between this and the free version of this game.

Copy/Paste from the dev's response in the release thread:
[i]
Think of the flash game as a VERY early prototype for this game. The main thing that carries forward is the concept of "the game is a vertical platformer RPG!"... everything else, from the structure of the game, to the skills, enemies and levels, is improved and expanded, and instead of opening cages and turning into heroes you rescue, you now pick from one of three randomly generated heroes, and rescuing heroes from cages adds them as helpful NPC sidekicks to the current level.
One big addition is local network multiplayer, as well as a new engine (it's no longer made in Flash!).[/i]

The original had the Mario-style headstomping, while this version has a proper RPG statistic style combat system, with min-max damage, health bars, and a lot of pattern variation on the enemies. Also, the Super-Mario-World style world map is gone, replaced by a linear progression of 10 different randomised levels before the finale.

Thank you for the info. ^_^