Kyogre: S, still strong and lack of permanent rain doesn't affect most variants, and the defensive set even likes the lack of 100% accurate Thunders. Specs still 2HKOes almost everything, we don't even have the lati twins now, and Palkia using Assault Vest shows how defining Kyogre is.
Arceus N: A. Arceus-N lacks initial power, doesn't give team support in terms of synergy but still a great sweeper. Stopped easily by burns and some checks, but it's combination of bulk and STAB ExtremeSpeed does make it unique.
Xerneas: A. Strong, versatile, and Fairy Aura is gay, but then Geomancy is a one-time use. The other sets are awesome, I like RestTalk Xerneas. The thing is Xerneas isn't as immediately threatening as Kyogre or Ho-Oh. I will place it at high A.
Ho-Oh: A, SR weakness is huge. Not good enough for S, one of the biggest threats, but still requires support. Defog is common now, people will expect for it, there are ways to harass the opponent, and pressure them. Defog doesn't work 100% of the time.
Yveltal: A. Strong Sucker, beast bird from hell. Gay Dark Pulse Flinch and the surprising power from the offensive sets, easy A but I won't give it S rank because it's weak to SR, and many common moves: Thunder, Ice Beam, Moonblast and Stone Edge.
You can ignore my post cause I just played a little bit of XY Ubers. I actually think Mega Blaziken is more threatening than Ho-Oh, it doesn't even need support as it's neutral to SR, and just one free turn, and mr.Chicken will KO almost anything. What are the things which can stop chicken? Talonflame? Azumaril? You will use Ho-Oh > Talonflame, Azumaril I am not sure, but it's so slow and isn't that bulky. Giratina forms are rare now, and a +2 Knock Off still does considerable damage.
Mega Chicken does take up a mega slot though so that sucks. No S for chicken. Outrunning Scarf Yveltal at just +1, that is boss. Voting Groudon for A rank, somewhere mid A, I don't think Groudon deserves to be so low as B, it can still run so many sets and supports Ho-OH.