I can understand that Water Arceus has good synergy with Groudon, but I would say that Palkia has better overall syngery. Groudon resists Rock, Poison and is immune to Electric. It is weak to Grass, Water and Ice. Grass: Water Arceus (x2 damage), Palkia (x1) Water: Water Arceus (x0.5 damage), Palkia (x0.25) Ice: Water Arceus (x0.5 damage), Palkia (x1) As we can see from above, Palkia is not weak to any of Groudon's weaknessess and resists Water more than Arceus. Also Palkia is only neutral to Thunder, which hits Water Arceus extremely hard from Kyogre. Both Palkia and Arceus hate switching into Thunder, but for Palkia it is less of a problem so we won't always have to rely on Groudon taking the hit (and rely on our opponent not predicting the switch). Palkia's only weakness is Dragon. Although Special Dragon-type attacks will kill Groudon and Palkia, physical ones would do less to Groudon thanks to its bulk and defensive EVs. tl;dr Palkia is great in Rain and Sun (as opposed to Water Arceus who is only good in Rain, really), has higher offensive stats, better synergy and is one of only four Kyogre counters listed in The Smog No18.