You kiddin' me? That Scizor was long dead after a volcano eruption lol. Anyway, the hardest I've played (so far) is probably Motochika's episode, where we have to stand up against Nobunage like a BOSS and beat up his BOSS Hydreigon everytime. The problem is we can't counter Hydregion without a BOSS Ice type, Fighting type or Bug type Pokémon, which are not easy to find in the lower left side of Ransei.
But I loved The Road To Conquest, because we get to BE the BOSS and KO everybody after a hard fight. It's especially dangerous because we are right next to Mitsu and Ieyasu who can both KO us.