Shedinja should rise to A, its insanely good with sturdy. Before you say it dies to stuff like sunsteel, moongeist, and status, if it didn't, it would be banned. It should be A rank factoring in these weaknesses. Primal Kyogre should rise to S, it males sense that it should be with the other two in the legendary trio, primal groudon and mega rayquaza. While I don't think this kind of logic works in standard, in balanced hackmons, the only thing that matters is stats and typing, which primal kyogre is not any worse at than groudon and rayquaza. Slaking should rise to A, its just as good as regigigas. Mega Gengar should rise to S, it's the best pokemon in the tier with normalize besides imposter chansey. Resgisteel should drop to B+, its much worse than zygarde-complete and giratina, and should be with aegislash. Mega Mewtwo X also deserves S, and arceus should be in a+ above regigigas and slaking. Kyurem-W should rise to b, its really good with 170 special attack and contrary draco meteors. Mega Slowbro is terrible, much worse than other waters such as kyogre, greninja-ash, mega swampert, etc. and should fall to D. Ash Greninja should take its place in B, its an absurdly good fast pokemon whos speed can be further augmented with speed boost or be given primordiral sea.
This is my first post, so please correct me if i made any mistakes. That being said, these points are all very valid and should be taken into account when the VR is next updated.
Welcome to smogon, and I am glad you have attempted to correct errors on VR. Unfortunately, some of the contents in your post has already been discussed in previous pages, so please allow me to clarify them for you.
Prior to 7th generation, the most popular way to eliminate Sturdy Shedinja was using a Mold Breaker Pokemon with Pursuit, which is able to hit Shedinja through Sturdy and land a hit using Pursuit even if Shedinja attempts to switch out. Although the introduction of Sunsteel Strike and Moongeist Beam has significantly reduced the usage of such strategy, "Mold-Pursuit" does not give Shedinja a second chance once it has switched into a wrong situation.
Yes, there are many number of ways one can hurt Shedinja. Weather damage from Hail or Sandstorm, entry hazards such as Stealth Rock and Spikes, damage from Poison or Burn, residual damage from trapping moves, removing its ability such as using Entrainment or Core Enforcer, and Sunsteel Strike and Moongeist Beam (two moves which ignores target's ability when calculating damage) are ways to hurt and eliminate Sturdy Shedinja. One must scout all these moves before sending in the bug.
Shedinja requires heavy team support to function, and one incorrect decision will lead to Shedinja instantly fainting.
While I agree Primal Kyogre has its prowess as the strongest Water-type, it is dealt easily with right ways. Let's start with the most common set, Poison Heal; the newly introduced move Core Enforcer will remove the target's ability if the target was hit last, and this is most likely going to happen since the most common users of Core Enforcer, Giratina, Zygarde-C, and some regenvest variants minimize their Speed stat and Poison Heal Kyogre's 98% of the setup move is Quiver Dance which boosts speed, making itself even more vulnerable to Core Enforcer's nullifying of an ability. Also, Spectral Thief is immediately going to shut it down and end the sweep by stealing all the boost.
Slaking is just a "different" Regigigas, and it is usually outclassed by Regigigas because of its worse special bulk which becomes crucially important when taking Boomburst from -ate users, setting up against opposing PH Kyogre, and others. Also, even if they are "basically the same thing", one can just look at Regigigas' roles, sets, and other things and apply it to Slaking. @ motherlove
Registeel is the most reliable and blanket check to -ate users with its fantastic mixed bulk, and it has 20 more HP stat than Aegislash. Both are not the same. Aegislash is immune to Fighting types and can be used as a nice imposterproofing wall for your own sweeper with abilities such as Flash Fire. They have different niche, but because of Registeel's overall bulk is much better, they are in different ranks.
Mega Mewtwo X, aka MMX, is an unfortunate legendary that is heavily reliant on its ability for wallbreaking (Technician, Mold Breaker, Stakeout, Refrigerate, etc.) unlike Mega Rayquaza and Primal Groudon, which is very self-sufficient with STAB moves such as Dragon Ascent, Draco Meteor for Mega Rayquaza, and very spammable V-create for primal Groudon which is way better offensive typing than Fighting or Psychic. Even as a mixed attacker or lure, Mega Mewtwo Y does much better job.
Arceus is not so hot 'mon to play with. It has 40 less Attack stat than Regigigas and Slaking which basically proves it is an inferior PH sweeper, and even the excellent bulk and speed are compromised by lack of resistances (such as how Giratina and Zygarde-C are top tier physical walls because of their great natural bulk
and resistance to Fire that lets them handle Primal Groundon).
Ash-greninja has possibly the worst infamy in Balanced Hackmons community due to Chopin Alakinoff's regrettable decision of using it as the latest BH clc core; It might look like it has good dual STAB moves and mixed offense stats, it fails to take a STAB hit from any offensive 'mons, and it is heavily reliant on boost to do an actual damage. The only niche of the frog was when Water Bubble was not banned, and even then, Primal Kyogre was the better user of such ability. Shell Smash Power Trip is outclassed by Mega Tyranitar / Hoopa-U / Yveltal due to its poor bulk that doesn't let it survive a hit and set up, and Sheer Force or Primordial Sea is outclassed by Mega Mewtwo Y and Primal Kyogre.
I believe you had right reasons to at least make a claim, but I am afraid to say that you have missed out reasons why aforementioned 'mons are in low rank despite their niche you have mentioned; we nominate 'mons into different ranks while regarding their strength and weakness, their efficiency in the current meta, and the number of viable sets (that is not notably outclassed by others) it can run.