Although Wallace's Champion chamber is a bit more pretty in my opinion and I enjoyed the addition of Juan as a Hoenn Gym Leader, Steven Stone was much better suited as the Hoenn Champion. Steven's team was a bit more diverse (while 4/6 of Wallace's team succumbs to "LOL Thunderbolt", with Ludicolo taking neutral damage from Electric-type attacks and Whiscash being completely immune due to being part Ground-type), and he even employed the 2 Hoenn Fossil Pokemon, Armaldo and Cradily, and the guy knew how to effectively use a Claydol.. Plus, Steven's signature Pokemon, Metagross, attacks ferociously with Earthquake while Champion Wallace's signature Pokemon Milotic just...Recovers a lot.. >_> Also, the influx of Water-type Pokemon League members did not help matters in Emerald (and alongside Juan and Wallace, even Glacia could count as a Water-type pseudo-specialist, as 60% of her team is Water-type, with the remaining 20% being the pure Ice-type Glalie). I know Hoenn has a lot of water and surfing and diving, but sheesh. >_>
If a Ruby/Sapphire remake is made, I would want it to be a mix of the Ruby/Sapphire and Emerald canons, with Juan as the 8th Gym Leader (his design seems to mesh well with the other Gym Leaders due to its vibrancy.. or something) and Steven Stone as the rightful Hoenn Champion. Wallace could be a roaming Trainer like he was in the Pokemon anime (maybe fought on the Abandoned Ship, as water likely contributed to the vessel's demise), with a Pokemon team possessing strength on par with Emerald Steven Stone's team (I still hope that Steven's Champion team gains levels during rematches, like what Pokemon FireRed/LeafGreen did with its "second wave"). This way, Steven gets re-instated in his appropriate position, Juan gets to stay, and Wallace brings a whole new spin on things in regards to battling..
EDIT: Wow, the poll is currently 8-0 in Steven Stone's favor.. XD