I don't know why people make a deal out of simply making the games harder themselves. People do realize gamefreak intentionally makes these games very optional so many different people can play at different levels.
Items-Healing items are a big thing. Using them isn't making the game harder, it's making it easier, and that's what it's there for. If you want a harder game, don't revive a Pokemon in a battle after it fainted, don't heal it at all with any items, use a move.
Numbers-I can only imagine the amount of people who do a 6 vs 3 battle against these NPC and will complain they never even lost one, I suppose the fact using more Pokemon then your opponent which is an optional choice to make the games easier for you doesn't really come to people's mind or anything. Why not use the same amount of Pokemon as your opponent.
Type Advantage-I mean seriously, do people use whatever is infront of them or something, do whatever option arises to them? Just because something is there, doesn't mean you have to use it, not everyone does drugs and that, not every jumps of buildings, yah I'm comparing that to a video game because it should require far less effort to not do something in a video game then those things. Seriously, type advantage is there to make it easier, don't depend on it if you want an actual challenge.
There are significant changes you can make yourself by simply not choosing to use easier methods. And even despite all this they still ended up giving you the Challenge Mode in the most recent games, poor accessibility aside, it's still there, you got your challenge, it'll probably only improve as time goes on to be more accessible and more challenging. Other then that, the game itself is fine as is, changing the "Normal" level to "Hard" would only push away their target audience, yah young kids aren't stupid and whatever, but for the most part they probably will be new to Pokemon, they wouldn't know what exactly to do and just go with it, they'd probably struggle a lot. Inexperience makes a game more difficult, experience makes it easier. I'm sure I had a tough time playing the first, second, third, maybe even forth generations, all because I never really invested any time in really learning all the details about how to make the game easier for myself. I had an easy time my first play through of White, but I over leveled way too much, leveling up 5+ levels between each gym really didn't work in the long run. I've played the fifth generations plenty of different times with plenty of different teams, with plenty of different difficulty ranges from really easy to annoyingly hard.
Pokemon games can already be already, if you just don't make them easier for yourself.
I think the only way they could make the game harder is to have the AI cheat.
Which people seem to think Battle Facilities do, I don't know if they are serious but, most people do go through a headache while dealing with the things. Which of course, if you want a challenge, there is that. That's pretty much there for those who want the challenge.