Not difficult to find, but difficult to survive and actually catch, and I'm surprised this one hasn't come up yet after nearly two pages.
You know how the cover legendaries of most Pokemon games are pretty easy to catch starting with Dialga and Palkia in Diamond and Pearl? Game Freak probably sets their catch rates in the 45 - 70 range so the player can viably capture these Pokemon when they encounter such a titan in the main story. Being able to snag a powerful Pokemon like Xerneas when you aren't even the Champion yet is an empowering moment. Unfortunately, the first time Game Freak ever FORCED an encounter with a Legendary as part of the story, at the time, you could not have chosen a worse Pokemon to fight than Groudon in Ruby or Kyogre in Sapphire.
These two are LUDICROUS to fight at this point. Not only do they have stats rivaling those of Mewtwo, but both of them have abilities which alter the weather in their favor for the ENTIRE battle unless you provide your own weather effect. Furthermore, Groudon knows Bulk Up, and Kyogre Calm Mind. It's no Recover, but boosting their own stats makes these Pokemon even more impressive threats than they already were.
All of this said, if you asked me whether one is more difficult than the other, I'd have to weigh things in Groudon's favor for a couple of reasons.
1.) Kyogre is a Water Pokemon, which means Net Balls are more effective against it, giving you more options to easily catch Kyogre. There isn't an equivalent Ball for Ground-types like Groudon.
2.) Kyogre's Drizzle compounds with its Water-type to turn Hydro Pump into a 270 power attack! However, neither Ice Beam nor Body Slam are boosted by the rain, although Ice Beam can become more potent through Calm Mind. As a Ground-type, Groudon is not gaining STAB from Fire Blast, and Fire Blast does come off Groudon's weaker offense. However, Drought grants Fire Blast a power boost anyway (180 power), and being a Ground Pokemon sizes Groudon's Earthquake more, the latter of which comes from Groudon's stronger offense. And with Bulk Up, both Earthquake and Slash get better. Basically, when you fight Kyogre, you're facing one lethal attack, while the other two are good or even meh. Groudon, however, has two dangerous attacks plus one which is still pretty good thanks to Groudon's high Attack.
3.) Drizzle doesn't defend from any of Kyogre's weak points, but Drought helps Water attacks fizzle out in this fight. TBF, Drought would make Solarbeam more deadly against Groudon, but who uses Solarbeam in-game?
One minor point in Kyogre's favor of difficulty, though: nothing in Hoenn is immune to Water and Ice damage (Ghosts are immune to Body Slam, though). Yes, Water Absorb was an ability in RS, but Poliwag, Lapras, Vaporeon, Wooper, and Mantine weren't in RS, so no Pokemon in Hoenn had Water Absorb. Meanwhile, you can find Pokemon who are immune to each of Groudon's attacks (Ghosts for Slash, Fliers or Levitators for Earthquake, Duskull for the previous two, Vulpix / Ninetales for Fire Blast).
AFAIK, this was still the age when you got one shot at catching the legendary Pokemon, too; if you blew it by KO'ing Groudon / Kyogre, tough luck.
It wasn't just that these Pokemon were difficult to catch due to low catch rates, nor is it just them being powerful. Groudon and Kyogre were two of THE most powerful Pokemon in the entire series when RS were released because they bend the game to their favor so much on top of being powerful regardless of their abilities. Making a boss fight like this MANDATORY in those games is absolutely brutal and a mistake which should not be repeated.
...which is one of several reasons why I think ORAS sucks.