They actually did the same thing in Johto and in Sequel Unova except they used Dragon instead of Water.
Yes, but the difference is that although Lance is a Dragon Champion, only 3 of his Pokémon are Dragon-types. The same goes for Iris.
Steven is a Steel Champion, but only 3 of his Pokémon are Steel.
Wallace, on the other hand, has a full team of 6 Water Pokémon. No diversity, and definitely no challenge after you know how to deal with Water Pokémon, thanks to Juan, the pure Water-type Gym Leader, giving you all you need to know of what to expect from Wallace.
It's for that reason alone that I'd prefer Steven over Wallace as Champion. And honestly, that's pretty much from where all the dislike stems: there is little to no challenge in fighting Wallace when you can just attack him with the same strategy used to defeat Juan.
As much as I love version differences, having the final boss be different depending on the game is a bit weird to me.
And before anyone mentions Drayden and Iris as different Gym Leaders in BW, the only difference between their teams was the genders of their Pokémon and the ability of their Druddigon. Steven and Wallace aren't even
close to having a similar team.
And Wallace being Champion is a feature of Emerald, and there's no reason for one game to have the Emerald champion and the other to have the RS champion; these are Omega Ruby and Alpha Sapphire, not Omega Ruby and Alpha Emerald. In HGSS, the Crystal elements were included in both games, so for ORAS I can safely say any Emerald additions would also be in both games.
I've mentioned it in the Juan thread, so I'll just post a digest version here:
I'd like for Wallace to be the 8th Gym Leader and for Steven to be the Champion of "story mode," and for Wallace to be the post-game Champion. Juan would take Wallace's place for Gym Leader rematches, and Steven can be found at Meteor Falls once the post-game begins.
