The EXP Share just makes things faster, not easier. It lets you achieve the same results in significantly less time. That's not easier, that's just less time-consuming. If you added in the same EXP Share mechanics to the games that don't have it, you'd finish them just as quickly. Time spent creates the illusion of increased difficulty, but that's still all it is: an illusion. I mean, think about it. If you grind up to level 70 in a "harder" game for the Elite Four - we'll say Black, which has a reduced EXP mechanic - it might take you 10-20 hours more or whatever, but you're still going to curbstomp everything with ease. It's exactly the same thing as an "easier" game like X, it just took you longer to get there. Try playing a Gen VI title without the EXP Share turned on and it'll take you a similar amount of time as your Black file took you. It's not actually any harder at all, but you THINK it is because you had to waste a ridiculous amount of time grinding that you didn't have to waste in another game. There is absolutely no correlation whatsoever between difficulty and length of time spent grinding in Pokemon games.
The changes made to the games over time are more quality of life changes than anything else - they're designed to streamline the experience, not make it easier. Streamlining means that you spend less time doing tedious, repetitive tasks, like grinding for levels. The gameplay mechanics remain the same, and the same rules apply across all Pokemon titles: know your type match-ups, outlevel your opponent, and you'll win. Amount of time spent grinding is immaterial to actual difficulty. Number of Pokemon your opponent has doesn't even make a difference either, because you can use as many items as you can carry, so the only difference between 4 Pokemon and 6 is that you may not have to use as many.
If you want to actually make the game more challenging, you're looking at things like:
1. A level cap. If you could only have Pokemon that were a certain level before you got the next Gym Badge, you'd create a more equal playing field, meaning you would eliminate the ability to overpower your opponent by grinding.
2. Capping the number of items and Pokemon you can use in a battle to match your opponent. Gym Leader uses 2 Full Restore per battle? So do you. That means you'll have to think strategically about what to bring, when to use it, etc.
3. Re-introduce the Challenge Mode mechanics from B2W2 - give Gym Leader's Pokemon held items, etc. It's a small thing on top of everything else, but with the above two conditions it would definitely contribute. Especially if their Pokemon's levels are 5 or so higher than the cap.
4. Restrictions of the types of items etc. you can use and hold, so you can't break the game by giving your Pokemon Choice items, etc.
5. Restrictions of the Pokemon you can use, on top of everything else.
Imagine if you could only bring one Fighting-type Pokemon into a Normal-type Gym, said Pokemon could only be Level 25 at most, the Gym Leader's star Pokemon was Level 29 or 30, and you both had two Super Potions and whatever held items were available at the time. Now imagine that Pokemon was Whitney's oft-reviled Miltank, which came with Milk Drink as it did in HGSS, and had Zen Heabutt for your Fighting-type Pokemon. Now you've created conditions which require strategy and tactics to overcome and might begin to approach difficult depending on what is available at that stage in the game.
Just changing the EXP Share mechanics and calling it a day does not equate to making a game easier or harder. It just determines how long it'll take you to reach the desired conditions (i.e. being overpowered) which you can achieve in ANY of the titles. Again, time-consuming =/= difficult.
Perhaps this comes from my experience playing JRPGs that are actually difficult, and my patience for grinding - I'm a Disgaea fan - but I see absolutely no difference between Pokemon titles and their difficulty. All I see is wildly varying EXP growth which means I might have to spend a little extra time gaining levels.