Rayquaza: Rayquaza is more limited than the current Pokémon in S rank. It can be great, but some battles it is also quite underwhelming. Rayquaza has a harder time against teams that aren't defensive from my experience, just hard to get an opportunity to set up. Look at all the current S rank Pokémon, he doesn't really set up against any of those. The same goes for the A+ rank Pokémon actually. It's just not as universally good as the current S rank mons.
Giratina-O: Giratina-O is one of the most important Pokémon in the tier. Shouldn't be A+ rank. It's by far the best spinblocker (Giratina is a huge momentum killer and Gengar is extremely frail) and checks a lot of threats. Also, it can be quite scary of its own. Pretty much no Pokémon can switch in on all sets safely.
Deoxys-S: No, sorry but it is not just 5-6. If you can get Stealth Rock and Spikes up in exchange for losing one Pokémon while they have no hazards and you get momentum, it's definitely worth it. Giratina-O being a great spinblocker and stopping literally every spinner means those hazards are staying up for good 9 out of 10 times, or more probably. And those hazards are great, that's on average around 25% damage on Pokémon switching out. (5x 25% is 125%, more than the 100% from being down 5-6)
Kingdra: I guess it could go down to A-. When supported properly it can definitely be scarier than Palkia though. It's not that hard to get rain up for the entire game, in which case this is perhaps the best cleaner possible. Just a beast vs offense, it does have some problems though vs Dialga and Groudon admittedly.
Deoxys-A: Not really a great revenge killer. Any priority will KO Deoxys-A with no problem, and it's not fast enough to outspeed most common non-priority sweepers either. DD Rayquaza, RP Groudon for example outspeed, while SD Lucario, SD Rayquaza for example KO easily with priority and don't care about ExtremeSpeed. If you use this as revenge killer, you're likely gonna have a lot of problems with those mons.
Deoxys-N: I don't think you understand what makes Deoxys-N good. You say it is outclassed by the other Deoxys forms, which seems the case, but it actually beats those in the lead. Versus Deoxys-S it has enough Defense unlike Deoxys-A to survive 2 ExtremeSpeeds, making it able to KO it itself, either getting a layer of Spikes (or Stealth Rock) and limiting Deo-S to one layer, or if it Taunts prevent all hazards from Deo-S.