Loved, loved, loved Digimon World 2, mostly because of f that DNA Digivolution level up system, but I could see how that wasn't explained very well, especially with a language barrier. I'm actually replaying it now, and while the rest of the game has flaws, I still like it.
I didn't really start gaming until I was 7 or 8 so I can't think of any think that stopped my progress, not progress stopping but I definitely didn't understand the drift system in Crash Team Racing, so I just played without it.
OH, I remember having lots of issues in Metal Gear Solid, specifically the damn radio code that was on the case, I just did not understand, but I'm pretty sure there were other moments where I got stuck too.
One of my younger friends got stuck in Pokemon Yellow, he did not understand why he couldn't leave Viridian City, so I had to help him take the package back to Oak so he could get his dex.