There are a few differences between the steam version and the itch.io version. First, the leaderboards do not work in the itch.io version because it relies on the steamworks api. So if leaderboards are important to you, please download the steam version instead. Similarly, the achievements do not work in the itch.io version either, for the same reason. However, it's not all bad. The itch.io version has no DRM at all, so you are free to play it offline and without any other additional software. All other features remain the same between the two versions.

Update: the steam version has been patched to v1.2. A small patch that fixes a weird sync issue that appeared with a Windows 10 update. This issue would cause the game to run slower than intended, making the game significantly easier. The itch.io version has not been patched yet.  I may release an update to the itch.io version eventually, along with a free playable demo version as well. However, most of my time is dedicated to a different project right now so this patch isn't a high priority right now.