I'm going to straight-up nominate Mega-Sableye to S rank because my god this thing is so incredibly good. It is literally the face of ORAS stall, and that's despite the existence of other Megas which literally just wall half the metagame. I mean yeah, you can run Mega-Slowbro and Mega-Altaria on stall and straight-up not have to worry about most of the tier, but Mega-Sableye provides something far more important than just beating threats, and that is control. Specifically, complete control over the hazards game, as well as control over status, over stallbreaking, etc... But it's mainly hazards. Entry hazards are one of the best and most effective ways of dealing with stall teams. You can have a team where every one of your Pokemon is walled by something on the opposing stall team and still win just by forcing the opposing Pokemon onto rocks several times, to the point where said counters are no longer counters. Sableye pretty much stops this from happening at all, which for a playstyle as passive and prone to get pushed around as Stall is priceless. Stall teams featuring Sableye pretty much invariably beat stall teams without Sableye since the latter automatically lose the hazards war which usually decides stall vs stall matchups (it also generally beats the opposing stallbreaker unless it happens to be Diancie which I don't think is really used on stall). Oh yeah and it also walls a massive portion of the metagame too, let's not forget that.
Also, what actually counters this thing? And I don't mean "switches in and beats it from there", I mean properly counter it, aka switching into it repetidely without any support. The only thing I can think of are Clefable, Sylveon, and Altaria. Everything else (Gardevoir, Tentacruel, Diancie, Talonflame) gets worn down by it. It's one of the most meta-defining Pokemon in the tier, puts in work regardless of matchup (even when there's a Clefable on the opposing team it still usually pulls its weight) and it requires specific measures if you want to actually beat it, and even then it can sweep teams without too much difficulty. It also has excellent synergy with a few really solid Pokemon on stall such as Tentacruel and Jirachi to the point where building around it is really easy. Right now the typical stall team is something along the lines of Sableye/Tentacruel or Empoleon/Jirachi (I know Jukain uses Doublade but eh)/Clefable/Chansey (or Blissey b/c Lando-I/Gengar are things that exist)/Skarmory or Chesnaught or Hippowdon some other physical wall, and for good reason.
Mega-Sableye is an absolutely dominant force in the current metagame and I don't really see why it wouldn't be deserving of S rank.
Oh yeah speaking of Jirachi.
I've taken up team rating recently (I swear this is going somewhere), and the single Pokemon I found myself recommending the most frequently was Jirachi. Now, this may well be just me, but I really do feel like Jirachi fits on a huge amount of teams in this metagame, being a staple on Stall and pretty much the best fairykiller in the tier in general, having excellent synergy with many new megas such as the aforementioned Sableye, Latias, and Altaria, and providing a ton of utility in general with Wish, Body Slam, Stealth Rock, U-Turn, Healing Wish... It's not just to be used on defensive teams and can be tailored quite easily to fit on offensive ones in general. It's also an excellent special wall in general and although it suffers from the popularity of Dark Pulse on Greninja, it's able to handle big threats such as Mega-Diancie (Earth Power doesn't do enough), Mega-Sceptile, non EQ MMetagross, and Mega-Gardevoir (who I've discovered kinda steamrolls a ton on ORAS teams). I'm really not sure whether it's A rank material or not (A- is still really high especially considering that it used to be unranked), but it has been putting a really impressive amount of work for me lately, so I think this still needs to be discussed.
Mega-Slowbro I'm not sure about. Crobro is not an A+ set imo, it's taken advantage of too easily and stopped by quite a few things. But a simple set of Scald, Ice Beam, Toxic/Thunder Wave, and Slack Off walls a ton of stuff, including MSalamence, without actually being setup fodder for anything really unlike CroBro (Sub Mence says hi!). However, I'm not really sure what kind of team you're supposed to use it on? It kills too much momentum for offense and you usually want a better mega that isn't just a slightly improved version of its regular forme, and you realistically aren't really going to use it on Stall because even if you're not using MSableye (which.. why would you not use MSableye?) MAltaria and MLatias are also great picks which differentiate themselves more in what they do from their base formes (you can run regular Slowbro and get more-or-less the same results)
also Magnezone, MAero, MLatias and MAltaria def need to move up lol.