You're echoing my thoughts exactly. Mine started out as a simple proof of concept using the CS area in Khan Academy and then I took it "offline" to flesh it out. That's when I started running into all of the complications you just mentioned; it really is a daunting task. I'm even struggling with a platform. It's HTML5 Canvas right now which opens up Facebook, and mobile using something like Phonegap, but I'm so inexperienced with both that I didn't think about keeping things responsive for different screen resolutions. Ugh!

I'm happy to hear I'm not the only one bumping into reality, though it definitely sounds like you're further along than I. I'd love to check it out once you've shipped.