If Palkia gets Waterfall, will Kyogre no longer have a use?
That'll be sad. Most powerful water Pokemon of "all generations" gets outclassed a few months later. What's next, Groudon?
Answers
The main niche for Palkia is that it is different from Kyogre. Not weak to Electric or Plant, but instead weak to Dragon and Fairy. It will probably have good but not great water moves, and probably won't be quite as good as Rayquaza with Dragon moves. It's a dragon that's neutral to ice.
But, as always, we'll see. Remember how Gyarados seemed to be a high CP miss, then it got Waterfall, and Vaporeon got knocked down a notch? We could get some of that here.
If Palkia gets a moveset as good as Kyogre, it will be a bit below in DPS but severely above in TDO against many targets. Double resistance to fire, being neutral to grass and electric coverage moves are very relevant qualities.
But Palkia can't learn Waterfall or any other water quick move that currently exists in the game. Niantic could always make a new one and I think they have the incentive to.
Groudon is actually at some risk of getting outclassed by gen 4 mons due to its trash moveset. If they give Garchomp a good moveset it would be king of ground in both DPS and TDO against anything except ice-move carriers.
In the long term Groudon and Kyogre are probably going to get access to their signature moves which will forever cement their place as top of their type in DPS.
Palkia only learns; Water Pulse, Aqua Tail, Hydropump and surf for damaging moves and they're all already charge moves in pogo. It also learns Aqua Ring and Rain Dance that are both status moves and liquidition which will more than probably translate into a charge move also. Its very doubtful that Palkia will get a double water set and don't forget, even if it does, Krogre can still learn Origin Pulse plus has its Primal forme, I think its safe.