Everything about Team Flare. They had the darkest goal in the whole series (and very nearly achieved it) but they're the most moronic, waste of space team I've ever seen. Lame Pokémon, crappy leaders, terrible outfits...they were just not threatening at all.
And also echoing everyone who said the Elite Four in XY, but I'd add pretty much every single Kalos gym leader in there. They're all pushovers, made doubly so by the fact that they stuck with the godawful "no more than three Pokémon for gym leaders, four Pokémon for Elite Four" standard they set in fifth gen. Not to mention, the Pokémon that they do have just aren't that great - Olympia having a Meowstic as her ace at the seventh gym (when you've been facing your rival's Meowstic the entire game) was laughable, and Wulfric even basically admits you can one-shot his entire team by breathing on them before he even battles you. As if that weren't bad enough, there's only one gym leader that has Pokémon with full sets of four moves - seriously, look it up on Bulbapedia if you don't believe me. The champion was a pushover as well.
Can I also add a quick note to say how absolutely anticlimactic the final showdown with Archer is in GSC and HGSS? He's the interim head of Team Rocket in the absence of Giovanni, you fight through a takeover of the largest freaking city in Johto to get to him, and when you finally face him...you get a team of three Pokémon - two of them being the weak unevolved Houndour and Koffing. Thank God for Drayano ROM hacks that actually fleshed out the Rocket story arc and gave it a proper final showdown.