In recent years I think Cynthia was the hardest champion, in DP. She was downlevelled a bit in Platinum, so first time around she wasn't so hard, but in Pearl.. Wow. Having a level 66 Garchomp was just.. aaaah. The first time around I didn't have any Ice types, so there was just no easy way around it. I guess Lance was pretty hard to beat in HGSS for his rematch, seeing as he had at least 2 Pseudo-legendaries, and they were all in their 70s. I guess in FRLG, Blue was pretty hard to beat for his rematch. And then Wallace wasn't too easy either.
I've named a lot of them but I guess Cynthia in DP was the hardest, overall.