I actually never had too much trouble with the champions. Strangely enough, it was often the lower Elite Four that gave me trouble. For example, long ago when I first got Ruby, I kept getting stuck on the second and third members. Once I beat the third Elite Four for the first time, however, I went straight past Drake and Steven pretty easily. I'd have to say overall, though, Cynthia would have to be the hardest. She might be the only champion I ever lost to on my first play through.