Fiddled with the organization of your post
You underestimate that Ekiller also holds together teams from being swept by stuff like Mega-Blaziken, who has no counters.
A scarfer can't put the offensive pressure on a team like Ekiller can- when you bring a scarf Kyogre in for the rk, you are only doing exactly that, when you bring in Ekiller for the rk you are also indirectly threatening with a countersweep. Since a scarfer has to be locked into a move and can't set up, they can always be taken advantage of. If you honestly think a "good old scarf vastly (!!!!!!!!!) exceeds" Ekiller in the area of revenge killing then I honestly don't know what I am supposed to think anymore. It is also cool to include the best revenge killer in the game as an emergency break against most sweepers- something no other mon can do.
Nothing can set up on E-killer and many mons are forced into making certain plays when it gets in just because how threatening it is.
Gengar isn't as much of a problem as you think. It's not always that easy to Mega Evolve earlier than E-killer who can bust up a mid-game mini sweep (it doesn't need to sweep end game, with a Life Orb it has the opportunity to get work done mid-game too). [snip] but it will always have to Destiny Bond to actually kill Ekiller, unlike what it has to do with vs Arceus-Fairy for example.
Gengar also destroys quite a lot of support Arceus, along with any slower mon really, [...]
I don't see any concrete examples of slow bulky team archetypes that E-killer sucks against. Just because a team is slow and bulky doesn't mean you can work your way through them. It's power is not underwhelming,
you just think it is because you have a conception that it is when in fact you actually never used the mon properly. If you use it for what it is best at- a focus on gluing teams together by providing offensive presence and revenge killing utility, and then focus on getting your sweeps- then you will see how good it is.
You argue that it has a huge opportunity cost. You should look at my argument for why the opposite stands true this generation. There is no singular Arceus-forme that can be argued to be better, most of them are really flawed with obvious weaknesses (Grass is Gengar-bait, Fairy is better but is also Ho-oh/Scizor weak depending on moves+Gengar-bait, Water is a cool compromise but it can't check Kyogre that well, Rock is a shitty typing other than for checking Ho-oh). You can argue that using a good defensive typing is is cool.
Well, no super solid counters that are currently being used. (I like to believe that the ubers metagame can still adapt to this threat but we'll see from spl I guess) Still, definitely a fair point and a plus for Ekiller.
I interpreted your revenge killing comment as to mean exclusively in the scenario where you need to stop a threat. Espeed is a strong useful priority but it pales in comparison to a Water Spout or Bolt Strike (plus coverage moves) when it comes to stopping threats. (with exception to those handful of really, really fast guys like blaze) As for the indirect pressure, that is certainly present but it's a separate thing (and its not absent from guys like Zek and Kyogre, you give them more chances to RK something and your checks to them are going to be worn down fast) as it deals with punishing a switch rather than stopping a threat. (you could use your bulk to stop the threat but that's obviously not revenge killing, and Ekiller can't really afford to have as much bulk this gen)
BU MMX can .trl (unless you are talking after ekiller has already boosted? Then you can use Skarmer and stack.)
I was talking about Gengar before Mega Evolving. If you don't run Jolly Ekiller (which is forced to use LO to not be super piss weak) then Gengar will still outspeed and can pick you off with Focus Blast. (252 SpA Mega Gengar Focus Blast vs. 200 HP / 4 SpD Arceus: 272-322 (63.1 - 74.7%) -- guaranteed 2HKO)
Yeah, but I'm not arguing support Arceus for S rank. :p Being weak to one of his main STAB/coverage moves would definitely be a concern for any Pokemon to be considered S rank.
Guys like wisp support Arceus, Lando-t/donner, Mega Scizor, Skarm, phys def Kyogre, phys def ho-oh, etc are all common metagame mons that can switch into and force out Ekiller if needed. Obviously, some are shakier than others but you also have to keep in mind how most of the remaining team is going to be Pokemon like Aegislash, Ho-Oh (LO), Amoongus (lol), and other random Toxic users that can take an unboosted hit and cripple Ekiller with a powerful blow/status. (you can argue that Lum helps with random Toxic and shit but that brings up my earlier point of Ekiller being harder to just use one set for because the new checks threaten it in new ways) There's not really many free turns for Arceus-N in this metagame and a lot of teams naturally have multiple checks to it. Sure, you can use teammates and all that but my point was to refute the concept that it became a superior sweeper this gen, I feel the opposite is true.
I feel like you are overestimating the gluing aspect. It's only really present if you need to check Mega Blaziken (which is important but early meta so I don't really like overvaluing this) as otherwise it's just another sweeper than can potentially pick off weakened threats. (a Mewtwo can, too, if the mon doesn't pump up its speed) That specialization is comparable to Rock Arceus, imo.
The opportunity cost is clearly there. It may be true for the other support Arceus formes as well in opting for them over Ekiller but none of them have been suggested for S rank. (and I personally wouldn't put any of them there)