I'm really torn. It's difficult for me to say that any one generation is definitely "the worst".
Gen 5 had the worst region design imo but the pokemon it inroduced and the story it told were great though the balance of these two is a little skewed. Black and White introduced so many new pokemon(which isn't a bad thing) and didn't ease players in at all with the inclusion of older pokemon in the dex, giving players(I should probably just say 'me') a bit of a jarring transition. This was fixed a bit in Black 2 and White 2 but is still present in the first games. The story was the same way and, while it was better than other tales told in the series, it did begun to cut in on the gameplay experience. The whole 'chosen one' motif is never something I thought would work very well with pokemon and in this instance it didn't. Being told that you were the one to command the dragon and seemingly take a hard stance on philosophical issues such as truth vs. ideals felt very limiting to the player's narrative freedom. What if I don't want to fulfill this recurrence of history while I'm taking down Plasma? Maybe I'm just making hyperbole on some things that have been inherent in much of the series...
Gen 6 introduced the fewest number of new 'mon to date. While this doesn't seem to be that much of a problem at first glance, there are 455 Pokémon in the Kalos Pokédex with 70 of those being unique to the region. That means only 15.4% of the Pokémon in Kalos are new, that's pitiful. Instead of making the region feel like a grand new experience with a band of new comers taking center stage it felt like more of a rehashing of older generations with a light garnish of new faces. Honestly, I prefer Black and White's influx of naiscent luster to X and Y's trickle, although neither are truly good. Another point is the fact that not many of the things in Kalos felt like you truly earned them. Just by using the mechanics the game presents to you and following the storyline, without even trying to grind your team to superiority, you will easily sweep the game without effort. The Exp. All and Pokémon Amie will make sure of that(with no Exp. Share alternative to the EXP. All, I might add). Granted, one is able to forego these features. However, the amount of things given to you seems arbitrary and is only worsened by these features. Here you go, two starter Pokémon for no reason, a Key Stone and a Lucario holding a Lucarionite to go with it. Bought the game in it's first couple of months after release like so many did? Have a Blaziken with its mega stone... Let the players earn things that feel like they should be rewards instead of things taken for granted, a certain level of accomplishment should be felt obtaining things like this and they shouldn't just be hints that are given out 'willy nilly' to the player as they go through the usual storyline romp, this causes them to lack a sense of value unlike rewards in other titles such as the Johto starters in Emerald's post game.
The antagonistic team in X and Y honestly wasn't terrible. They felt a bit more like Team Rocket... only a bit worse. With team rocket we knew what their goal was, they wanted to exploit Pokémon to gain wealth and we as the players wanted to stop them because we(presumably) cared for Pokémon. For the majority of the game my encounters with Team Flare left me wondering why I was fighting them until late in the game it was revealed that "Surprise! We're going to kill everyone who doesn't have our sense of style!" and that was the only moment when fighting against the team was actually compelling. Granted, they do have the most interesting looking leader. Lysandre's up there with Archie.
Lastly, the Kalos region, for all it's relatively interesting region design, gives players little reason to travel around it after the 'main game' is over. Kiloude, Lumiose, and the Day Care are the only places you'll really need to be visiting after you become champion, making the post game relatively lifeless. Compare this to DPPt or RSE in which players were traveling to multiple locations after their league victory, chasing down secret areas, roaming or secret Legendaries, and rare items or Pokémon. Or compare it to GS and their remakes in which players are given what is essentially an additional league challenge to go through with Red's battle atop Mt.Silver being a cherry on top(though some would criticize the levels of the Kanto pokemon and the general lack of much other than the gyms, which is an issue).
All in all, I can't really say that one is the worst but after writing this, Gen6 isn't very high on my list. Which is why I'm hoping they'll do something g unexpected with it's third version or sequel(s) and introduce more new Alos Pokémon and more interesting things to do and a better storyline.