Well, first of all: Kanto's Elite Four are just as good, with high levels, not actually sticking to their typings (Agatha, Lance), and a mixed Champion (Blue). Lance's Dragons are almost impossible to defeat with under-levelled teams, and you'll no doubt use so many items that it's really hard to fight Blue. I'm one of the billions of people who thinks Lance is awesome too. But lets be honest, he's much better with three Dragonites (That somehow levelled down upon evolution :P) and a Charizard (The greatest starter of all time).
However, I prefer Hoenn's Elite Four, for various regions. Firstly, they were my first Elite Four. Secondly, they have brilliant pokémon. I mean, Sidney has some lethal attackers in Absol, Shiftry, Crawdaunt, and Cacturne, and his Mightyena's Intimidate makes it even harder to defeat them, particularly as Fighting and Bug are physical types. Phoebe's Ghosts are really tough - three defensive behemoths, two who pack a punch (Dusclops), and one with no weaknesses (Sableye). Banette are really lethal, and not only is this team tough to take down, but with a combination of Pressure, Protect and Grudge, Phoebe successfully removes most of your PP making it that much harder to battle the others. Glacia does pretty well considering the many weaknesses of the Ice-type, and I personally love all of her pokémon. Drake's dragons are equally as tough to take down as Lance's dragons, and his Salamence is possibly more destructive than Lance's Dragonite. Oh, and Wallace (I played Emerald), despite being a mono-type champion, is extremely tough. I mean, you have Wailord with its' massive Hp and Water Spout, Ludicolo with Double Team and a sole weakness to Flying, Gyarados with its Intimidate and general destructiveness, Tentacruel and Whiscash with their odd combination of weaknesses - one is immune to Electric, the other isn't weak to Grass, and Milotic, the godly pokémon with a massive special defense to counter its' two weaknesses and plenty of attacking power too.
The fact that in Emerald you then get to battle Steven at even higher levels than Blue's team, in a region where no trainers stray above lv.60, and only gym leaders on their limited rematches and the Elite Four hit lv.50+, means that Hoenn's Elite Four and Champion, particularly if you include Steven either in RS or E, with his epicly defensive Steels and Fossils, are really tough still. Combine this with my own personal love of Emerald and the part of my childhood it represents, and Hoenn wins hands down for me.
