Groudon. You want reasons? There is a full essay on this somewhere else on the site, but I'm too lazy to look it up, so here is are some of the more important points.
Drought>Drizzle
Drizzle only powers up Water and makes Thunder 100% accurate and both of since Kyogre is both Water and uses Thunder, it is useless for other Pokémon.
Drought on the other hand powers up Fire and lets Solar Beam only take one turn too charge. Since Groudon is Fire and never uses Special attacks, both are very usefull for other Pokémon on your team. Exeggutor with Chlorophyl, Solar Beam and HP Fire is really powerfull in the uber metagame.
Drought also halfs Kyogre's Water attack's power, while Drizzle does nothing to Groudon's physical attack's power.
Swords Dance>Calm Mind
Sword Dance raises Attack by two, Calm Mind raises Special Attack by one and Special Defence by one. Kyogre doesn't need the Special Defence, but does need the Special Attack. Groudon doesn't need Defence, but does need Attack. Therefor, it seems obvious that Groudon also wins in this catagory.
The uber metagame is also filled with Special users, so a physical sweeper>special sweeper in the uber metagame.
Rayquaza sucks most of all. It's 4x weakness to Ice really kills it hard. So does Groudon with Swords Dance and Rock Slide.
There already are lots of Flying legendaries, some Water legendaries and some Dragon legendaries, but only one Ground legendary. And that is what makes Groudon unique.
Also the design, a blue wannabe Orca, a green flying snake with a few things sticking out from it's body or a red heavily armoured tank.
In short: Groudon>Kyogre>Rayquaza battlewise, but Groudon>Rayquaza>Kyogre designwise.