The proper answer is either Colosseum or XD. Double Battle-focused games where the opponents used actual strategies, where your own team selection was limited to most of the poorest 'mons to ever come out of Johto, and where you had to catch Pokémon in battles where they had partners that kept pommeling your 'mons.
As for the core series games... none of them are really that difficult. There's the ridiculous level jump in GSC between Gym 8 and the Elite Four, with no places to grind, which makes the Elite Four challenge quite hard... or rather, tedious to prepare for.
The reason why we feel the difficulty is decreasing, can mostly be attributed to our own experience. We learn what the mechanics behind a Pokémon's power is. As kids, we'd teach Alakazam Mega Kick, or Machamp Fire Blast. We'd happily believe that a move's power increased the more we used it, so we'd keep Thundershock on Ampharos instead of getting Thunderbolt or Thunder. We only had a vague idea about the type chart, never mind what the type of the various Pokémon were. We'd do so many mistakes that the games became challenging, but with the knowledge of a grown Smogonite, the games are a matter of "use the right move to OHKO the opposing Pokémon". We'd never dream of using suboptimal moves, or specialize our 'mons at the wrong end of the attacking spectrum. We build teams and pick moves to cover all our bases, when we see an opponent Pokémon we instantly know which moves would be the best to use against it.
To put it simply: We're too well prepared for the Pokémon games, and they mainly rely on the players' (lack of) preparation to create difficulty. Save from self-imposed challenges, the only way to have difficulty in Pokémon is a lack of preparation, and we're well past that stage.
This is definitely a good point, but honestly I'm not sure how true it is. While we are prepared for newer games now so the overall difficulty of the franchise has decreased compared to when we were kids, we're all still very capable of replaying the older games with the preparation and practised skill that we as a community now possess. Difficulty does primarily lie in game design, and this is notably different throughout the franchise.
This topic can easily just be a "the boss fights are the hardest ergo it's the hardest game", but we all know that Pokémon is more than that. Distribution of Pokémon is a major factor, and diversity of major threats for each gym leader is also important. For example, in Emerald you get Pokémon like Lotad, Wingull and Shroomish quite early on who can all sweep Roxanne very capably -- and 2 of the 3 starters can do so too. Generation II, however, is much more different with Falkner only really being combated by Geodude and arguably Gastly. While we, as well learned smogonites, can just say "oh, let's head into Dark Cave and grab a Geodude", a lot of players won't think about that or just won't want to. For me, this means that Generation II has a much harder beginning to the game. I will also point out that Viola is in a similar position over in Kalos, but her team is genuinely weak. The Surskit hits like a water boatman trying to sink the titanic and the Vivillon isn't much better. BW2's Cheren is irrefutably the hardest first gym leader: no Fighting-Type Pokémon before it besides Riolu, who didn't learn any Fighting-Type attacks until Level 15 compared with Cheren's Level 13 ace. The best Pokémon to use against him is Azurill with Charm, which is a reasonably complex strategy for the first gym in the game.
Therefore, while we might still be knowledgeable players, it's easy to deduce that BW2 has the most difficult first gym. That's why I don't think this topic can be shrugged off as you did by saying players have improved more than the difficulty curve of the franchise, and there's a lot of discussion to be had here.
Personally, I think that Generation V are home to the most difficult games. Whether BW or BW2 is the hardest I'm in two minds about. Lenora is IMO the hardest gym battle in the franchise with few legit counters (Boldore or Sawk/Throh are about it; Pignite is decent but not bulky enough to take the Retaliate) and Elesa is also a big killer as she Volt Switches between something with only a Ground-Type weakness and Emolga, which are immune to it. However, beyond Elesa, the game gets much easier as the available Pokémon become more versatile and gyms grow more generic. BW2 has harder gyms throughout and, while there are more versatile encounters, these encounters don't necessarily equate to actual good options -- especially against gyms. You still don't have a major threat to Roxie by the time you meet her and she's a relatively tough fight. Marlon is the hardest 8th gym in the series except probably Claire, which is a feat when there are so many options available to take him out. I think this is mainly due to there not being that many options in the local area, but really for teams to not have Grass- or Electric-Type Pokémon by the 8th gym is kinda rare.
The notion that the OP presents is IMO untrue. The Pokémon franchise hasn't been getting easier as it's grown. However, I agree that Generation VI is pathetically easy, and actually I have friends who will agree, if we need another way to combat Codraroll's suggestion. I have friends who got introduced to the series in Generation VI and beat those games easily, but they downloaded Generation III to their phones and they found them really difficult. They still don't know the type chart off by heart, but they could easily make their way through Generation VI in spite of this. There has been a major difficulty decrease in XY and ORAS and it's a big issue if the franchise continues to be overcasualised.