For me the most tricky part of development is to create a full keyboard gameplay (instead of default mouse point&click).
But I also had a challenging time in Catyph to create the spaceship arcade minigame. It's a very simple game, but there were a lot of things to prepare carefully: asteroids collisions, countdown, game over or victory, score, etc.
You can try an old prototype here if you're curious: http://bit.ly/2jsSaxi
I also tried to include realtime 3D characters in Visionaire from 3dsmax, but I think that it doesn't work well. I really admire some of you here who decided to create games with this feature. Congrats guys!