I preferred Steven as Champion. I think Wallace was a better character than Juan and should've stayed gym leader, as the guardian of Sootopolis. I don't remember Wallace's team very well, but I think a good Electric Pokémon should solo him easily. Granted, Blaziken owns Steven's team (something I wasn't really aware of until the last fight...), but Wallace's weaknesses are more glaring IMO.
Anyway, the canon of the games past Emerald is quite confusing, considering the change in gym leader and champion. In HGSS, which is known to be later in the timeline than Emerald, Steven calls himself the champion of the Hoenn region, which is weird considering the protagonist of Emerald already beat the champion by that time. Yet in B2W2, both Wallace and Steven participate in the PWT Champion League, denoting Emerald is canon after all. So who's supposed to be champion?
I believe the change happened as a nerf to Blaziken. Blaziken's both types could maul Steven's Pokémon, whereas there were things in Wallace's team Sceptile couldn't get past easily.