As far as the actual battle and challenge goes, Steven is the obvious choice. I mean, he uses many different types on his team, despite having a preference for Steel types. It takes a truly well-crafted team to take him down. Wallace, on the other hand, is just a typical Water trainer. I never really understood the reasoning for making him champion in Emerald.
Either way, Steven is still the true champion of Hoenn. Its just like the second generation. The "champion" you go against after the Elite Four has the personality of one, but the true master lies far ahead with a team so leveled up and diverse that no ordinary player can beat him. For this reason, I have never seen Lance as a champion, but only a poser meant to make the player want more and eventually get more (Red), just like in the first generation. The same goes for Wallace in Emerald; his title means nothing after you go to Meteor Falls and find Steven, ready to fight you in a truly pressing battle.