Even though it doesn’t learn Water Gun, Niantic can give it that and Aqua Tail. (It can learn the aforementioned charge move) This will keep Kyogre as the best Water attacker, while Palkia trails by a small DPS margin. Now I will tell you the pros of and cons of both, they should be about equal.
Kyogre Pros:
Higher DPS
Better for Solo and Duos Of Tier 3-5 Raid Bosses
More damage at once (Palkia may faint after two Aqua Tails, while Kyogre faints after a Hydro Pump)
Better bulk vs Ground and Rock types
Kyogre Cons:
Harder to dodge with
May faint with a partially charged bar
Has some weaknesses that limit its performance versus certain raid targets
Palkia Pros:
Has better TDO than Kyogre VS Fire Types and bosses weak to Water that have Solar Beam (This helps in Entei, Moltres, Ho-Oh, and Groudon raids)
Can dodge easier
Set is more flexible
Better for gym battles (Less energy wasted)
Palkia Cons:
Less DPS, which is crucial in raids
Aqua Tail outputs less than Hydro Pump (Kind of like Outrage Vs Dragon Claw)
Doesn’t have an advantage versus Ground and Rock types
(The graph is VS Entei)