Oh boy I hope this post doesn't end up being too long.
First off, regarding their outfits...if they receive a slight change, that's fine, but don't change the idea. It was brilliant--
"We at Team Magma want more sun! Time to put on these hoods, leg warmers, partially black clothes and...oh no we appear to have melted."
"We at Team Aqua want more rain! Let's dress like pirates, with thin clothes, no jackets...oh dear is this the flu I've caught?"
Now that that's about of the way, in terms of their story relevance...
Each villainous team leader has been "evil" in their own way, which is one of the things I love so much about Pokémon.
Giovanni is driven by greed; he knows he's bad, and doesn't care. He realizes his actions are "evil" and even admits it, but as long as he gets his money he doesn't lose any sleep.
Cyrus shows psycho/sociopathic tendencies and claims to want to put an end to strife but shows more desire to control the universe than to bring an end to suffering. He had a sad childhood and his character is the result of various bad influences.
N is doing what he thinks is right for Pokémon, and is truly a good person--he simply got caught up with the wrong people, and is one of the most (if not the most) complex, interesting, and powerful characters the series has ever had.
Ghetsis is mad, with a lust for power and a disregard to both people and Pokémon (we've had people be abusive to Pokémon in the past, but to people! To his own foster son! That's really a big topic for any Pokémon game to handle). Arguably the most evil character in Pokémon in terms of just...pure evil-ness.
Colress is so neutral it's amazing. He only misused Pokémon because he thought it would bring out their true potential. But explain to him that being nice is the way to go? "Oh, I'll try that out instead."
Lysandre is warped, with good intent but taken to the extreme. Although it conflicts him he refuses to let go of his ambitions. A very tragic character.
And then there's Maxie and Archie.
During RSE, the villainous team(s) are painted as sinister, but in reality they're just doing what they think will benefit the world. They're not like Cyrus--Cyrus was the sole person benefiting from his plan. Maxie and Archie thought everyone would benefit, they just didn't realize it. They're so engrossed in their "heroic plan" that they fail to see the negative consequences they would bring. And once their plans are enacted, they actually understand the true impact of what they've done. Unlike Lysandre, who knows what he's doing is wrong, but still goes through with it, Maxie and Archie see their mistakes, admit their wrongdoings, and ask for help in stopping what they've started. Some people may call it silly, and in a way it truly is, but it makes Maxie and Archie surprisingly complex and even relateable--we've all thought something would be good for us, only to find out it was a bad idea after it's too late. It's only "silly" because of the scale Maxie and Archie take it to.
If ORAS can paint Maxie and Archie in the light of characters who want to fix the world but can't see farther than a few feet, they can become even more complex and even likeable. They weren't necessarily dislikable before (unless you just didn't like the whole "save the planet" stuff), but they didn't play up the strengths of their characters enough to give us something to really enjoy from them (unless you're like me, and you read into everything with way too much fervor).
Another thing that I really want to point out is their dynamic in RS. I know I'm probably the only person who prefers RS over E, but hear me out: in E, all that happens is that they're both evil. Two misguided men with opposing ideals and the power to bring their plans to fruition. It's powerful, to be sure, but in RS one of them was good.
One of them though to himself, "Wow, this team doesn't realize what they're doing. We need to put a stop to them!" and gathered a whole group of people to counter their plans. Remember how epic it was when in BW (almost) all the Gym Leaders stood up to Team Plasma? That's what one of the teams did in RS.
In addition to having a good but misguided evil team leader (which is already interesting in and of itself), we had a counter-force who stood strong against them, battled them head-on at Mt. Chimney, and assisted you, the player, in thwarting their goals. This dynamic is unique even to this day in the Pokémon games, and to see it played up in ORAS would be amazing.
They could really give the player more opportunities to interact with the good team leader, offering more insight into their character, behaviors, and personality. There could even be more interactions between the two leaders, both during the story and post-game. That would allow us to see them while they're enemies, and after they've essentially "made-up." They can focus on their regrets and perhaps even make the two bond, turning the evil team leader into a redeemable character.
Another thing that would be so amazing is if Maxie and Archie had different thought processes, different ways of speaking. Instead of making them say the same thing but one says "land" and the other "water," they could really be unique and you'll get an even more unique experience depending on which game you play. It would also deepen their characters even further, and make them stand out instead of being generic.
As to whether or not this will occur, I can't say for sure. They may be remakes, yes, but they don't have to remain exactly the same as their origins, so the possibility for playing up their characters in certainly there. I really hope it happens, because Team Magma and Aqua tend to be regarded as the worst teams because of how absurd their goals were...but in reality, they're some of the best if not for the sole reason of them actually achieving their goals...and they also have the opportunity to become some of the most interesting, well-written, complex characters of the series simply stemming from their misguided nature.
I know it may seem like I just repeated information that everyone knows about, but the reason why Magma and Aqua are so overlooked is because, although it was great at the time, they weren't given enough complexity for people to really think much of them. All that text I typed? That's complexities that are there, but are overlooked because they're not taken full advantage of in the original games. By playing up their unique roles in ORAS, they could move up from being "the joke teams" of the Pokémon world.
It would be a tragic missed opportunity if these characters were not given the depth they deserve.