You have very good points, but my question is why have they risen, I mean, all the things you said, excluding Clefable's Knock Off were already in XY,
and these 'mons have raised their ranks just recently, if it was a little after ORAS release I would get it.
Also, Clefable is bulky and versatille but it's offensive power is pretty lame, compared to such heavy-hitters that are in S Rank,
it's Def is kinda low so it needs a quite some EVs to have a decent Def, if we look at it's stats we'll see there is nothing really fantastic,it's Speed is bad, although that's the least of it's problems.
It's overall stats are just decent, it doesn't have a single stat that is base 100, so far I don't think Clefable is really that good to be in S Rank
You've also got to take into account that XY OU is a very different metagame to ORAS OU and the placements here reflect the current state of the metagame, as opposed to how good they are on paper, if I'm not mistaken. So while all of that was indeed in XY, the meta's changed considerably since then. I won't bother explaining Clefable as Bludz covered that in the post above me, but I'll try and shed some light on Volcarona and Weavile (and if I'm wrong, someone please correct me, I'm new at this in case you didn't guess)
In XY, Volcarona was at either C+ or B- iirc. The trends that accounted for this include:
Talonflame - generally regarded as one of the best mon in OU, not only was it a hard stop to Volcarona but it would also have been silly to use both one the same team, due to their shared common weaknesses (not least Stealth Rock) - you may as well just have used Talonflame on it's own and it was on pretty much every team, hindering Volcarona's usability substantially.
Mega Pinsir - was also on every team and could nuke Volcarona with Aerialate Quick Attack, only requiring a little prior damage at +0. Or if Volcarona hadn't already boosted it's Speed, Return would nuke it as well.
Basically I could have summed up the two points above as Birdspam generally, since it was a very effective playstyle in XY and Volcarona really didn't like it.
There was also:
Stealth Rock - Volcarona has a huge weakness to it (bear with me, I'm about to explain the flipside to all this in ORAS)
Mega Charizard X to an extent: Hidden Power Ground could only 2HKO this beast at +0, whereas Zard X could OHKO with Flare Blitz at +0.
Fast forward to ORAS, and 2/4 of these problems are pretty much negligible (Megas Pinsir and Zard X are rare). In addition, the rise of bulky Psychics such as Reuniclus, Steels such as Mega Scizor and it's resistance to moves such as Mega Gardevoir's Hyper Voice which have also become more common in the transition has only served to make Volcarona even more of a powerhouse today than it was yesterday. Basically, what I'm saying is Volcarona hasn't been buffed per se in the transition, but it can take advantage of the new metagame trends to become an increasingly dominant force thanks to the reasons Bludz posted above.
Regarding Weavile, basically everything Bludz said and also I'm not 100% sure but I think the dominance of Tanky Garchomp, Gliscor and Landorus (and, at the risk of repeating Bludz, the rise of other things such as Torn-T and offense generally) played a huge part in this. What Weavile has over other Ice types is an incredible speed tier and STAB Knock Off. In addition, and I could be wrong here, but I don't think the combo of Knock Off + Icicle Crash + Low Kick was legal in XY, and that's a very good combo to have typewise, especially considering the STAB Knock Off (this is pretty big). It also helps that it can run Poison Jab or Pursuit if it wants. So again, Weavile takes advantage of new metagame trends, but the STAB Knock Off and recently even more flexible fourth slot which lets it hit whatever the hell it wants also probably played a part in getting it moved up.
All I say on Clefable is that S-Rank is not reserved just for the Pokemon that shit on all the other Pokemon with their raw offensive power, and echo what Bludz said in the post directly above.
Forgive me for the long-ass post.
TL;DR: new metagame trends in ORAS compared to XY, in addition to being very good Pokemon anyway, are the primary reasons why these Pokemon moved up. Although they themselves haven't changed much in the transition, this is a new environment now, and one which is far more favourable to them. The rankings reflect the situation of the metagame currently and how well each Pokemon thrives in said situation, rather than how powerful or not individual Pokemon are on paper(if this was the case Mega Ampharos would probably be somewhere in A, for example. This is just an example to try and make the point clearer, don't hurt me guys).
