Braid and The Witness, his last two games, both used custom engines written in C++.

Then it's a good thing not everyone listens to traditional advice.

I mean, it's not like there are no games in existence that shipped with a custom engine.

Even in hindsight it's hard to judge whether building your own engine was good or bad decision, and we are nowhere near "the hindsight" level of knowledge.

Last I heard, the Sokoban game has a ridiculous number of puzzles on it. Can't find a source but I seem to recall hearing that it would take 400+ hours to finish it all. So.. I don't think it's entirely unreasonable it's been taking this long.