Sigh... Dragon's really tryna make me work on this one ovo.
Alright...
Firstly, Blizzaga is countered by Thunder. Both are absurdly powerful moves that are "super-effective on the opponent. Difference is, because Leviathan can fly, and probably will to avoid stuff like Earthquake, Precipice Blades, and Fissure, and given that even in Final Fantasy, people are aware that flight counters earth attacks given Titan's quote, it makes him a sitting duck for Thunder. And if Leviathan causes it to rain, Thunder is going to be even more of a problem. Meanwhile, Blizzaga can be lessened by Flamethrower, Fire Blast, and Lava Plume. And before you call foul, Ice is weak to Fire in both series. And Kyogre naturally learns Ice moves, so it knows to be cautious around them.
Both are equal in AP, but Groudon is the only one with means to boost itself via Bulk Up. And there's still the dice roll that is Ancient Power.
Both can heal, but Groudon is the only one who can do it effectively. Not to mention that Spring Water is probably gonna have less effect in the Drought.
When it comes to experience, well...Leviathan's age is unknown, though Leviathan is quite likely as old as Groudon. Experience comes from the fact that Groudon is bitter rivals with Kyogre, who's pretty much Leviathan without the time powers. Meanwhile. Leviathan just ranks above Titan, who's essentially Groudon.
Speaking of time powers, it's probably important to note that in FF, they're pretty much the same as Agility and Scary Face, just that they're slowed down/sped up via time, rather than statistics. Different application, same result. Groudon's innate speed advantage + Scary Face + Mud Shot + Rock Tomb lessens its usefulness.
While Leviathan can heal status ailments, there's still that moment where it's still affected. Paralysis is much more serious on the healer, given the inactivity factor (paralysis exists in FF, btw) preventing potential healing. And given that statuses can stack in FF, burns become a problem.