Okay, so from my personal experience it goes a little something like this:
12. Pokemon X/Y
These two games are enjoyable, however with so many Pokemon in the region along with the EXP. Share, it is so easy to beat it within a week of casual playing. At least the Pokemon introduced in these games were cool, and I enjoyed the region's aesthetics.
11. ORAS
Honestly, the reasoning here is similar to X/Y in the sense that you can utilise the EXP. Share. Also, aside from maybe 2 - 3 major battles, there is no moment in these games (with or without the EXP. Share), where I have struggled.
10. Red/Blue
I decided to separate R/B from Yellow since you have the luxury of choosing a starter Pokemon. Maybe it is my memory playing up, but I cannot remember these games being hard at all. At least, not anymore. Grinding isn't really needed for the most part bar the final stages of the game, and there are so many weird glitches and bugs that can be abused. At least there is no EXP. Share
9. Fire Red/Leaf Green
*Copies and pastes above reasoning* Really for the most part, aside from some glitches and mechanics being fixed, they are pretty much the same as the originals, and they were certainly not any harder.
8. Black/White
Although there were a couple of gym leaders that would mess me up if I was unprepared (Elesa), I found that there isn't any real major difficulty. Ghetsis and N at the end of the game are tough, however, I will admit that.
7. Ruby/Sapphire/Emerald
These games have an amazing soundtrack, great Pokemon, memorable character designs and an amazing cool champion, including Wallace. However, again, aside from a couple of gym leaders and elite four battles, there wasn't any real challenge.
6. Sun/Moon
Being the newest installment, I thought this would be a cakewalk with the EXP. Share, but I was pleasantly surprised by how tough some key NPCs are, such as Hau's Alolan Raichu, and the majority of the Trial Captain/Kahunas. I lost my first ever nuzlocke to Ilima on the docks, and I have been too traumatised to try again since.
5. Gold/Silver/Crystal
These games aren't hard in the traditional sense that they challenge you, but more so because of the weird scaling they used for various areas. One minute you are crowned champion after having a genuinely tough battle with Lance. Then the next minute you are in Kanto trouncing low leveled wild Pokemon, or vice versa in some parts. Less challenging, more unfair.
4. Yellow
Only this high because i forgot about it. Well, more so because you are forced to start with Pikachu, who cannot use it's STAB moves against Brock. As such, you are stuck trying to catch and train a Nidoran/Butterfree/Mankey just to beat the first gym, and in the old games, that can take a while.
3. Black2/White2
The only thing stopping these games from getting any harder is the fact that there is such a diverse Pokedex. You can catch Pokemon such as Riolu very, very early on, which can be a major powerhouse for smacking gym leaders out of the way. I found the level scaling to be fair, not forcing you to grind too much, but also not causing you to repeatedly lose a gym for being slightly underlevelled.
2. Diamond/Pearl/Platinum
These games were slow, but challenging, which probably makes them seem even harder to beat, since they are so hard to play. Most key characters in this game are genuinely strong, such as Cynthia, Barry, Roark, and Cyrus. Also, I find the legendary Pokemon in these games to feel stronger than others for some reason.
1. Heart Gold/Soul Silver
Takes what made the original games challenging/unfair, and kicks it up a notch. Whitney still stomps unprepared teams, Claire's Kingdra still 1-shots every non-bulky Pokemon in existence, random NPCs have really strong Pokemon for some reason, and Lance has 3 illegal Dragonites who will kill you if you do not have any counters. Plus you have the long grind to challenge Red, and although he is fairly simple to beat once at a high enough level, you need to spend a while mindlessly battling others to get there.
All based on my personal experiences, of course. :)