Because Masuda's favorite type is Water, Kyogre is incredibly unbalanced compared to Groudon.
Here are some comparisons
>Kyogre gets STAB on Surf, Hydro Pump, and Water Spout; this is super effective on Groudon, and is boosted by Rain.
>For coverage, Kyogre gets a better BoltBeam with 100% accurate Thunder off its great Special Attack
>If you're not going Speced it also can use Calm Mind to an amazing effect.
Meanwhile
>Groudon, for what it's worth, gets amazing STAB Earthquake - but it's not boosted by Drought, and it's not super-effective on Kyogre - not to mention its only 10 points above Surf
>It's Water Spout equivalent, Eruption, is both Special and Fire-type, so it can't fully use its Attack and its ability; it's better off using its Hydro Pump equivalent, Fire Blast, which suffers the same issues, or, at best, Overheat.
>SolarBeam is obviously designed as a coverage move for Groudon to use against Kyogre, but again, it's a special move, not STAB, and completely useless if its raining.
>Other moves it can use are the unreliable Stone Edge, the low-powered Dragon Claw or Rock Slide.
>It suffers from four move slot syndrome and has to choose between coverage, buffs like Rock Polish or Swords Dance (whereas Kyogre can simply use Calm Mind and boost its two relevant stats), and debuffs like Thunder Wave, Toxic, or Stealth Rock.
Groudon simply ends up much harder to use and usually gets fucked by Kyogre; it can beat Kyogre if used properly, but if used by two evenly matched opponents it will lose.
Fuck you Masuda.