Please look more at the definitions of the S-rank before claiming that Pokémon don't belong there (talking to you Frog).
S Rank: Reserved for Pokemon who can sweep or wall significant portions of the metagame with little support, and Pokemon who can support other Pokemon with very little opportunity cost ("free turns"). Also the home of Pokemon who can easily perform multiple roles effectively, increasing their versatility and unpredictability. If the Pokemon in this rank have any flaws, those flaws are thoroughly mitigated by their substantial strengths. If there are suspects, they will come from this rank.
If you look at it, Kyogre practically defines this. It can sweep a significant portion of the metagame by holding the item choice scarf, it can break walls with choice specs, break stall (somewhat) with a bulky mono-attacking calm mind set. It can very much support other pokes with little opportunity cost, which is here defined as free turns. And Kyogre's ability drizzle makes its team supporting skills come in an instant, not by wasting a turn.
Kyogre performs multiple roles, all effectively. Examples are, choice scarf and specs, defensive or specially defensive, thunder-wave lure, hell even chesto resto is workable. And not to matter the tweaks you can do to lure usual counters, like using CM Water Spout to lure Ferrothorn or specs T-wave to crap on Palkia/Latias.
So we have realised it can perform a lot of roles effectively, your claim is that its counters are popular. But one has to remember, there is no such things as a Kyogre counter. Latios doesn't have Latias bulk to take on brutal onslaughts over and over again, and Latias is prone to being set up on by Ferrothorn, as even HP Fire fails to deal significant damage in rain. This leaves us with the most practical Kyogre check IMO, Palkia (Choice-less) which can combat Ferrothorn switch ins (since the durian is a common partner to the whale, we must discuss what is actually happening when a so called "counter" to Kyogre switches in). But Palkia will be worn down, and a predicted thunder deals good damage and has a 30 % paralysis rate.
Giratina is obviously also set-up bait for Ferrothorn, as well as Arceus-Water.
Now what are Kyogre's flaws. Well, to me there are none, because even though Kyogre is kinda slow, choice scarf remedies this. Its defense is also a bit low, but Crogre has okay defense so even that is not really much of a flaw.
Kyogre practically defines the S-tier.
E-killer is above others because 1) It is the perfect sweeper. And that is alone the reason why it should be S-rank. Arceus-Normal can never be hampered that much by paralysis, something that makes other sweepers jealous. The only status stopping E-killer is burn, but remember that the move Will o wisp only has 75 % accuracy, which is unreliable (not to mention that if E-killer holds Lum Berry, the probability of two hits is 56.25 %).
It sets up on pretty much anything not super effective, or drastically overpowered (specs Kyogre, Reshiram, and Kyurem-W for example) and proceeds to sweep.
Looking at the defintion for S-rank, I can see where your claim is coming from. Arceus-Normal can't perform too many roles effectively (well Wallceus isn't really anything special) but the fact that even considering another Arceus forme for a team makes a tough choice about opportunity cost, as E-killer is such a brainless and good addition to almost any team.
So we have found its flaws, it can't really do to many things, and E-killer is indeed predicable, but its definitely S-rank even considering the criteria because:
If the Pokemon in this rank have any flaws, those flaws are thoroughly mitigated by their substantial strengths.
Its substantial strength in sweeping makes all "flaws" it could have in versatility unimportant, since after all, it is the perfect sweeper.