What do you see in Darkrai over Yveltal? Obviously higher Speed, Nasty Plot and Dark Void are great qualities for a Pokemon, but as a god, you're giving up two great recovery options, a ton of bulk and an entire type option for the team.
Not every team can really cope with Darkrai's presence at all. It's lightning fast, with few OU options able to outpace it without a Scarf, it can mostly-reliably buy itself a turn with Dark Void to then Nasty Plot, making it
extremely difficult to manage a switch in on it, particularly since it can predict an attempt at a Sleep fodder switch in and often 2HKO whatever tried to absorb the Sleep, many teams have little or no access to priority, let alone priority effective against it/strong enough to substantially threaten it, etc. It's
incredibly threatening when it's in your face, and not every God has anything to use as a hard stop to it. (Not a Fairy God? No Clefable for you)
If I'm building a team and my God's utility in the fight itself is a low priority, Yveltal is definitely superior. Darkrai edges out Yveltal in ability to pressure the enemy team and potentially grab a sweep, often even when the enemy team has suffered little or no damage.
Dark Void + Nasty Plot is another of Darkrai's highlights, but it's predictable, not extremely reliable (as accurate as Stone Edge for comparison) and Darkrai's sweep is ended by strong priority or a physical scarfer. If you really want to use Sleep status, Yveltal has flying types who surely can learn Hypnosis or Sleep powder or something.
Wait, there's Flying types that have Nasty Plot alongside highly reliable Sleep now, and enough Special Attack and a good, widely effective Special STAB to abuse this all with?
Dexsearch says: no, no there's not. Crobat (Hypnosis) and Chatot (Sing) are the only Flying types to even
have a Sleep-inducing move and Nasty Plot. Neither of them comes
close to Darkrai's 135 Special Attack. (Though Chatot's access to Boomburst
arguably makes up for this)
The point of Dark Void is that it allows Darkrai to initiate setting up and sweeping on anything that isn't immune to Sleep, isn't Magic Bounce, and doesn't carry Sleep Talk. It's not simply about Sleeping a key threat, though it can do that
too.
Not every team
has strong priority. Groudon has nearly no access to priority of any kind, for instance, being limited to a couple of Ice Sharders, a few Sucker Punchers (Only Golem and
maybe Dugtrio being sensical to run it on), and three Quick Attackers, Diggersby being the only one that's even slightly notable for potentially using it. Note that Breloom, Infernape, Magmortar, and (
hah) Ledian are the
only Pokemon in the
entire game that have Mach Punch that aren't pure Fighting types -so Fire, Grass, and
technically Bug and Flying teams, in addition to Fighting teams, can bring to bear a Mach Puncher to hard-stop Darkrai. Other priority is not necessarily strong enough to be a problem.
Grass? Grass is kind of shit for Gods and Followers, with the only Uber Grass types being Shaymin-Sky (Tried it, it's not very good) and Arceus-Grass. (Has much better options to be running) Ledian is awful, period. That leaves Fighting and Fire teams -and frankly Darkrai's fear of Fighting types is pretty obvious (Mono-Dark and all) and something its team will be constructed to account for, presumably. (Blaziken, Mega Lucario, and Arceus-Fighting are the only Fighting-team Gods, and in my experience the first two tend to struggle and nobody has ever fielded the last one that I've seen. Might give it a shot myself, honestly)
The Scarfer, meanwhile, can't switch in directly, safely. (Oh, and Scarves are generally unused on stall and semi-stall teams) If Darkrai KOs something before you can get the Scarfer in, it's done work. Being a Dark type, it's not even that scared of Pursuit, poor Physical defense or no, and, again, many teams don't even have access to Pursuit anyway.
tl;dr version: There are multiple Gods that Darkrai can murder them+their team where they have a devil of a time successfully implementing checks or counters of any kind, let alone bringing them in to check/counter Darkrai without suffering a casualty somewhere along the way.
Yveltal is less matchup-influenced and has more diverse teams, of course, and in particular is more resistant to offensive pressure, but I don't think Yveltal simply crushes, singlehandedly, entire otherwise-viable teams the way Darkrai can.
---
On Kyogre vs Primal Kyogre, I also feel like Kyogre is generally the better God, enough so to justify dropping Primal Kyogre a star. It can support a Rain team, and its Scarf Spout sets are murderous against non-Primal Groudon teams. Primal Kyogre has the ability to switch into Primal Groudon and shut off its weather, of course, but that's iffy -Primal Groudon can 2HKO Primal Kyogre with Precipice Blades, while Primal Groudon can switch in on Primal Kyogre's Special attacks a lot more safely, so the advantage Primal Kyogre has against Primal Groudon is smaller than you'd think.
The other God close comparisons I have no particular opinion on.