Personally I feel the simplest ways to make Pokemon games harder are Set mode (you don't get to switch out for free every time you faint an enemy) and not overleveling the enemy.
Also, not relying on too much setup, like buff moves + healing items, or x items + healing items and then sweeping.
Also, there are rom hacks that are much harder than regular games.
The most popular ones (that I know of) are the Kaizo ones (Blue, Crystal, Emerald Kaizo).
I've seen a couple videos. definitely very hard, but I'd never play them.
They literally put 10+ forced trainer fights in every route, and each one is legitimately challenging.
Thinking of going back to heal 15 times just to walk through a route is not my idea of fun.
There's also Nuzlocking, which obviously makes things even harder