There is not at this time a way to save games to the Kongregate server. http://www.kongregate.com/games/kidgamez/enigmata-2-genus-revenge used a clever workaround of our /docs/kongregate-apis/shared-content-api to get a save game system working, but it isn't really designed for that, and unfortunately is ActionScript3-only, so it won't work for Unity3D. To save, most games just use local save games, or if you have your own server you can save them there.

I can't personally recommend anything, but I would check out "OSFlash.org":http://www.osflash.org/projects and their projects list to see some options. It looks like Sepy might be a solid option if you're looking for a FlashDevelop alternative, though it's just a code editor. The full IDEs don't seem to be as strong in terms of options - SencylWorks really might be one of the best for the Mac.