* Rather than saying to hit 'R' to reset have a button (keyboard can work too, but only allowing the keyboard goes against the rest of the game which is mouse/touch driven).
* On the right have the words "Goal" on top of the image, maybe put a box around it or something to separate it from the other images that appear.
* For the first level you need a "pit of success". Limit the available functions to only the one that works.
* The first few levels need to introduce and teach the user how to use each and every function separately. Say for 12 levels the first three teach/introduce a concept, the next 6 are actual simple/medium levels and the final 3 are the more difficult (but not impossible) levels before repeating and introducing a new concept.
* When you solve it don't put the message up top in little text, but next to the program and bigger bolder so the user knows. Ideally with some sort of css transition.
* When you solve it put a link to "Play next level" or automatically go to the next level after a short animation or something
* Only expose levels after you have beat them.
* After doing a function rather than instantly showing the next cube put a .5 second opacity transition (or something) so the user will notice what they did.
Lastly, but most importantly play test in person. Show someone your game, but don't say a single word. Write down everything they do wrong and debate how you can improve it and try again. Do not give them advice on what to do. If they can't figure it out neither will a ton of random people on the internet (I didn't the first time I saw the game and just closed it as I didn't realize I had to drag it over and I was on a tablet and saw the 'R' command and figure there was other keyboard only commands.)
Remember it is not fun to lose. Hard is fun, but you want to guild the user to have fun, be challenged, and build on the game concepts you have taught them. It isn't fun to give up because you have no clue what to do.
If you build in a way that users can create puzzles and share them (say by putting the user generated level in the url) the game would have more life as users spread the word by showing off their creations.