They should change the way they approach challenge mode then. I think a lot of people would love a harder region. I don't see why it can't be done without breaking rules. I feel like the remakes should be harder as Pokemon has a lot of loyal fans who have grown up with it. I imagine most people who buy remakes played the older version when they were younger. It would be nice to see a more challenging remake for those who played so long ago.
Its not just Game Freak. Pretty much every game company in existence has this problem. The only way to really do it is to artificially increase the enemies' AI, stats, and movepools.
Saying "I want more challenge" is easy. Actually sitting down, and making said challenge is really hard. Pretty much no company has gotten it "right" because more challenge often means making the game grueling.
For the sake of argument, lets say you decide on increasing all enemy trainers' levels by 10. Well the player can just as easily decided to overlevel themselves. So instead, you then decide on giving enemy trainers increased stats. This is frequently argued against because then players complain about this enemy being too hard to beat. A more competitive movepool and mons? Sure... except you're still limited by the relatively meh ones you found in the early game.
And here's another issue with that: what if a 6 year old who played X one time turns on "Challenge mode" because they think they can handle it? Then you have to deal with the wrath of overzealous parents who are angry that their precious snookums got his butt kicked. It might seem silly, but no one wants to deal with a lawsuit (even a frivolous one) because it damages the brand.
And then you have to actually think of the practical nature of that. If there's two story modes with different teams, you have to have the time to actually make it. And when your publisher (Nintendo) is breathing down your neck to get it out already, you have to ask if it would actually benefit the game.
Lastly, this was attempted once. Gen V had an unlockable hard mode. It was also criticized for many of the things I mentioned before: player facing OP mons with higher levels while forced into mediocre ones that were available at that moment, level disparity, AI being a cheating b... While some liked it, I really didn't see many people using that mode and those who did were "meh" at best about it.
This is seriously a no-win scenario. As I stated before, this game is not targetted to you or me. The part of the game thats meant to challenge older players is the post game and competitive PVP. Thats the hard work for adults. The storyline and fantasy? Thats for the kids who got this game for Christmas, and that's their target audience.
We're a periphery demographic and their way of appealing to us is stuff like giving the old Gen I starters Mega Evos or adding subtle adult storytelling in places like New Mauville, or adding ways to make the competitive post game much easier to break into. Doing more to appease older fans and aligning the series to appeal to them? Sure. Making what is essentially a second version of the game in the game for them to be challenged? Probably not worth the time and effort, especially when you look at many of the other features that would like have been cut to do so (Delta Episode? PokeDex+? Contests?)