To be honest, the hardest hack I've played is Pokemon Vega.
This is mainly because the important battles are really difficult. The first gym leaders were brutal.
The Bug-type woman's Shuckle is way too bulky, and you have to overwhelm it to beat it, cause of the healing items. The Rock/Ground/Fighting dude's Hitmonchan is brutal. You want to use Poison-types? Boom, Psychic Punch. Want to use Ghost or Psychic-types? Boom, Shadow Punch. The water gym leader has a Starmie that's extremely hard to beat, but aside from that it's not that bad. But that freaking Porygon-Z? My god. I'm not finished with it, but I think it will get a bit harder. And also, you have like 5 or so grass types (Pot-in-a-plant, Cherry mon, Abomasnow, Exeggutor and the starter (Which thankfully I got with Thick Fat)) before the Elite Four, and the others are reserved for post-game. (Breloom, Lilligant, some other Fakemons) However, since the game has a very good post-game (At least from what I've seen), it would be interesting since many of the Pokemon are post-game. That's kind of nitpicking, but whatever.
Honorable mention goes to Touhoumon Emerald. (This weird version that is just Emerald with the Touhoumons, no major changes or anything)