He's in my heart.
Yo I totally would have added him. I don't care that these remakes have "Ruby" and "Sapphire" in the title; HGSS implemented Crystal's Suicune subplot (and other elements) into their primarily GS story, and ORAS actually did try with the Delta Episode to incorporate Rayquaza's involvement, so I don't buy the whole "They're not Emerald remakes" argument. Juan totally could have come back.
Here's what I would do: have the main story of the game play out as it did, and proceed with the Delta Episode. Once that was all done, you'd start again in your room. Your mother would call you down because three guys are there to see you--it's Steven, Wallace, and a new guy, Juan! After your mother expresses concern over Wallace's attire, they'd say they have something to tell you. Steven claims he wants to just look for rocks or whatever it is he does in whatever cave after that whole ordeal in the Delta Episode. So--Wallace is going to be taking his place as Champion if the player ever wants to challenge the Pokémon League again. This other guy is Juan, Wallace's old mentor. So Steven's gonna be in the cave place that he was in in Emerald, Wallace leaves for the Champion room, and Juan tells you that he has something he wants to show you, so go meet him at the Sootopolis Gym when you have the chance. Once there, he challenges you with the Sootopolis Gym rematch team, and once you win, he explains the system to challenge the Gym Leaders again, which has now been unlocked.
Bam! Now you've got not only Gym Leader rematches back, but you also get to play through the main story as it was (kind of) in RS, you still get to experience the Delta Episode, and you've got Champion Wallace, Rock-Searcher Steven, and Gym Leader Juan just like in Emerald in the post-game.
...Now all we're missing is the Battle Frontier...