Greninja from B- to B
I feel like Greninja is a really underrated Pokemon in Ubers. I use it as an Offensive Spike Setter to good success. It has very good speed and can usually set up a couple layers of Spikes before death. If Spikes are not an option, it can always deal heavy damage with Hydro Pump or shut down opposing leads with Taunt. Overall, I think Greninja is just as good as the Pokemon in B, so it should move up.
EDIT: Thank you for clarifying. I was just confused as Ditto is normally a pretty bad Pokemon.
I'm really not sure about this one. The only thing that Greninja does that Deoxys-Attack doesn't do better is set up Toxic Spikes and I'm not sure if most teams really need an offensive Toxic Spikes user in place of, say, Forretress, who can use Rapid Spin and Explosion to block hazard removal for one turn. For regular Spikes, Deoxys-Attack hits hard, has better Speed, and has access to Taunt just like Greninja so I don't see why you'd use this Pokemon over Deoxys-Attack for this role except for playing games with Protean. I'd say that B- is perfect for Greninja and I don't see the need to move it anywhere.
Giratina-A C+->C- or D
Giratina has an extremely hard time functioning in this metagame, if it can even function at all, simply because it only has a defensive presence against a few mons and is a free switch to many of the more common threats. It wiffs extra hard vs Stall, Magic Bounce balance, and Offense because it cannot touch Mega Sableye or Mega Diancie with Diancie actually beating Giratina and Sableye creating a weird stalemate. Stall appreciates Mega Sableye much more than it does Giratina-A as Sab actually has a bunch of utility to offer in place of Gira-A's titanic bulk, Pressure, and lack of utility. Giratina just doesn't do anything is its problem. Although its bulk and Pressure sorta keep it from being entirely outclassed, it is still rather close to being unusable.
Arceus-Fighting C-->C
Unlike Giratina, this thing actually does have a use and I have found two builds it works on so far. Stopping Arceus-Rock from spamming Judgment against sand based Bird Spam teams is pretty big when the mon also soft checks E-killer, paralyzes many of its offensive switch-ins that hate paralysis, and has a decently powerful Judgment and Ice Beam to work with considering it is one of the few Arceus formes that can actually run maximum Special Attack. It basically does nothing against stall which is a bummer since it doesn't even beat Blissey, but against variants of Ferrothorn stall it can at least attempt to break Lugia's Multiscale in order to force a Roost and give a free switch to a partner. Its ability to paralyze Latias and Latios as well as 2HKO 248 / 204 (no boosting nature) Primal Groudon after Stealth Rock is also great for a Primal Kyogre partner as quite a few team structures use Groudon as the Kyogre checks, and the eon as a pivot in order to set up Harsh Sunlight against Kyogre. Now, this thing probably should not rise above C + because it is still a rather mediocre Arceus forme for many obvious reasons, but I do feel like it is better than what is currently in C- at least. Perhaps a C+ nom would be feasible because of where Arceus-Ice, -Elec, -Grass, and -Poison are placed? I feel like I am being too lenient with just C because it is better than Lucario, Chansey, and Kyogre. C is a good starting place at any rate.
Seconding the Giratina drop. This Pokemon literally sits on the field and looks pretty due to it needing Rest, Sleep Talk, and Will-O-Wisp on the same set. It's huge bait for Xerneas, Darkrai, Primal Groudon, Refresh Mega Salamence, etc. and it quickly becomes too pressured to Rest and is an unreliable phaser.
Arceus-Fighting moving up is an interesting idea. I'd like to see it in C because it does have some utility, resists Stealth Rock, beats Arceus-Dark and Darkrai, and works on certain builds. I could also see it moving up to C+ since it seems to have about as large of a niche as the C+ Arceus formes like you said.
I know it's been said before, but Mega Gengar should move up:
A --> A+
1. Mega Gengar has three really solid sets so it is very versatile and each set is really customisable so that you can patch up weaknesses to your team and give the other members opportunities to set-up. For example, a fast Taunt is really good right now like it has always been due to how set-up heavy Ubers has always been and it takes a ton of pressure off of team mates against HO, Disable ruins Ho-oh (a Pokemon that many teams struggle against), and Substitute and Hypnosis variants are incredibly scary to face if Hypnosis hits since it 2HKOs a lot of the meta game, forcing your opponent to sacrifice a Pokemon or two to break the Substitute.
2. Mega Gengar is also the best Pokemon in Ubers for patching up a team's
match-up weakness. Weak to Stall or bulkier Balance builds? Perish Trap/SubHypno destroys those. HO got you pressured? Offensive Mega Gengar variants can relieve so much pressure on your team mates against stuff like Darkrai and Extreme Killer.
3. Perish Trap variants avoid pursuit trappers such as Tyranitar, the biggest bane to most sets meaning that it can beat its usual checks while retaining utility.
4. Mega Gengar beats every Arceus forme (though some do need to be taken down with prediction). Many Arceus formes on balance glue those together, so losing it early can be devastating!
5. Mega Gengar does not need much supporting. He largely does his job solo, making him easy to fit on many teams.
Obviously Mega Gengar isn't the perfect Pokemon because it prevents you from using Mega Salamence and can force trades against Offence. These are both true, but Mega Gengar fulfils such a different role than any Mega Salamence set does that there are a variety of teams that would be better with Mega Gengar than with Mega Salamence so the opportunity cost, while something to thoughtfully consider, is not as pronounced as some people like to think. Concerning him forcing trades, you get to choose the trade that you force with Destiny Bond, giving you the advantage. Paired with dangerous threats such as Extreme Killer, Arceus-Ghost, Rock Polish Primal Groudon, etc. can mean that one key Pokemon KOed on the opponent's team can mean that the game is over.
Overall, I think that Mega Gengar's utility, versatility, and ability granting it a very different niche from Mega Salamence's warrant a spot on
A+.