As a kid, I found the Ratchet & Clank games to be relatively easy, but the final boss battles were always way tougher. Most of them got much easier when I replayed the series, but the one from the first game was extremely difficult because buying ammo during the battle was necessary, and it was very often that you'd run out of ammo, and then run out of money not long after.

I also found it really hard to beat Sonic 3 when I was younger, and I needed my sister's help to get past Ice Cap Zone. Sonic Heroes was worse, though; I struggled to beat the final boss as the team that are effectively 'easy mode' because of how quickly it attacked. In fact, it wasn't even technically the final boss, because you needed to beat it as all four teams in order to unlock the real final boss. To this day I still haven't done that, although I'm getting closer. I can't imagine how tough the final final boss would be, though. :P