I haven't really fought against Yanmega outside of the suspect ladder and I didn't find it to be much of an issue there. It was on Hyper Offense teams for the most part, which is about the only playstyle it fits on, but I never felt threatened much. The Speed Boost set - the only one I encountered - lacks power and while it seems like a decent cleaner in theory, weakness to common pririoty and the inability to OHKO a lot of mons coupled with a crippling 4x weakness to SR meant it always fell short of doing much unless it got a lucky flinch or two. Can't really give much input on the Specs Tinted Lens version but it does seem scary on paper; considering I didn't even use resists to take it on, I'd wager it would feel underwhelming, though. I honestly think Yanmega is fine where it is.
Now onto a nomination of my own that might be a bit controversial... I would like to nominate Sacred Fire Entei to S Rank. It is a really fearsome wallbreaker, and a stupid one at it. Sacred Fire is its main selling point, given its 50% burn chance, and it allows Entei to do a lot of things I really feel it shouldn't do. With Salamence's absence, its main checks are bulky Water types. But not all of them are good checks, and I'll illustrate here why:
Gyarados and offensive Mega Swampert disqualify themselves as good checks because they do not want to get burnt under any circumstance as it cripples them and keeps them from doing their job. Regular Swampert can come in on a Sacred Fire, but if the burn kicks in, it now has to choose between clicking Scald to weaken Entei and throwing Stealth Rock. Considering the second Sacred Fire won't put you into Torrent range unless you crit, Entei can also tank one of your Scalds so it can sacrifice its health to make sure your Swampert isn't much of an issue anymore throughout the game. Having to choose between SR and getting a kill mostly because of a burn is really, really stupid. But it's not just Swampert! Tentacruel suffers from much the same problem, and being unable to use a physically defensive Tentacruel to abuse a fire type doesn't seem all that fair. Considering you will likely need Tentacruel to spin and/or throw Toxic Spikes, it is imperative to run another Entei switch-in alongside it and decide on a case-by-case basis which one you'd like to fodder off to burn first.
Even the more defensively oriented water types do not appreciate Entei at all. Bulky Rest Mega Swampert as well as Suicune are both forced into a two turn sleep to regain their health and remove a burn, not only losing momentum but turning them into worse checks for other scary Pokémon such as Mamoswine or opposing Mega Swampert. On top of that, they're usually very clearly the Entei switch-in on a team, making it easy to double out on them, losing momentum guaranteed. Speaking of momentum, there's a water type that's all about gaining that: Alomomola. The reason anyone would use Alomomola is not only because it is a fantastic Mamoswine and Entei counter, but also because of its ability, Regenerator. Alomomola can throw up wishes and pass them with relative ease on many physical attackers because it can keep itself healthy thanks to its ability. Here's where Entei comes into play: if SR are up and it gets a burn on the first try, Alomomola will lose around 40% of its health on switch-in. Now the fish Wishes, loses at least another 27% of its health and faces a dilemma; should it pass the wish to a teammate, losing a significant portion of its own healthy in spite of Regenerator, or should it protect to keep itself healthy, losing momentum? If it chooses the former, additional physical wallbreakers as well as Flare Blitz are gonna have a field day with it if it tries switching in again. If it chooses the latter, it just lost momentum and gave a free turn to any Pokémon not afraid of its Scald/Toxic (and, if a player is gutsy enough, even Scald can't deter them). This fundamentally undermines the whole reason to run Alomomola, a Pokémon so bulky it should never even come close to fearing any physical fire type attack. The only truly "good" answer to Entei is likely Milotic, which can work with a burn due to its ability, Marvel Scale.
There aren't many non-Waters that cover Entei. The three that spring to mind are Arcanine, Chandelure and Snorlax. Arcanine and Chandelure both dislike Stealth Rock and fear Entei predicting their switch-ins and clicking Stone Edge whereas Snorlax does not appreciate the burn; a banded version with Facade can likely do damage unless Entei is paired with a ghost (in which case the burn screws it over) whereas the more common Curse version is forced into Rest, losing momentum much like Suicune. Both Flare Blitz and Stone Edge 3HKO Snorlax after Stealth Rock damage, while Extremespeed needs very little chip damage, leaving you at the mercy of Sleep Talk if you want to continue checking Entei.
So that covers Entei defensively, for the most part. How does it fare vs offense? If it did badly against offense, I wouldn't be bringing it up for S Rank, but there are a few key factors that make Entei scary. The first would be its switch-in opportunities. Offense has taken to running Pokémon such as Cleric Sylveon (which hits harder than Pixie Plate Whimsicott, by the way), mixed defense Bronzong or Calm Mind Cresselia, all of which cannot do much to Entei, barring Thunder Wave on Cresselia, and are mostly good for their ability to act as a pivot. Pokémon such as Doublade or Whimsicott have existed as glues on many different kinds of Offense builds for a long while, yet they can't do much back. The plus side is that if these Pokémon are the only ones Entei can come in on, it is easy to anticipate and double out to an Entei answer (or U-turn in Whimsicott's case). The downside is that a gutsy player might see this coming and just not switch out to Entei in the first place, so any player will have to gauge risk and reward carefully. Either way, there is no denying that Entei does get opportunities to click its STABs vs Offense and with Mega Aerodactyl being the typical fire resist, Sacred Fire gets to do work.
Entei's merit vs Offense does not solely lie in its ability to click Sacred Fire once, maybe twice a match, though. What makes it really shine here is a move it received in an event two generations back: Extremespeed. While this move forces us to run an Adamant nature, its usefulness makes up for it and then some. Whenever any Pokémon on offense sets up, they have to be careful not to take enough chip damage to be in range of Entei's Extremespeed or they risk getting revenge killed. Considering the frailty of most fast Pokémon, the ones priority is used for, getting some chip damage is usually not a tough task to fulfill. And with rocks up, maybe a layer of Spikes if you run those, softening up a team and cleaning up with Entei's extremespeed is very much achievable.
One of the things I mentioned a lot are Stealth Rock aiding Entei, but at the same time, is Entei not also weak to Stealth Rock? Indeed, and that is one of its few faults. Stealth Rock turns many would-be 2HKOs such as Celebi's +2 Psychic, BandApe's CC, or ScarfShao's HJK into OHKOs. Forcing Entei to take Rocks more than once opens up even more possibilities of beating it. Just the same, I think this fault is overexaggerated with Entei as it has a fantastic match-up against most Stealth Rock users by itself. SR Celebi does not take kind to any fire move. Mamoswine does not like running SR but also gets OHKO'd by Entei's Flare Blitz (even if Entei cannot switch in but I saw this match-up mostly when I lead Entei, and even Sash Mamo, a set which I believe to be extremely bad right now, fears a Sacred Fire burn). Cobalion, again, hates fire type moves. Offensive Nidoqueen risks getting OHKO'd by Flare Blitz, which is a 62.5% chance against the currently popular 128 hp 128 speed set. There is a slightly smaller chance to OHKO Empoleon, which has similar bulk but generally runs more hp. Swampert can throw rocks on Entei 1v1 but it has a hard time switching in, as illustrated above. Azelf usually only runs SR in its lead set, and it can get seriously screwed over by the burn as it won't get to knock something off or explode afterwards. Bronzong doesn't just lose vs Entei, it's a pretty much free switch-in for it. Forretress hates running SR but it's in a similar spot to Bronzong. Metagross loses to Fire moves and Entei can likely switch in once even if it clicked Earthquake (it needs a very high Earthquake roll for EQ + Bullet Punch to KO, if it even carries Bullet Punch). Gligar hates a burn and isn't particularly strong in the first place (and has to decide between defogging and SRing anyhow because running both never ends well). The only mons that can truly, reliably throw SR in the face of Entei are bulky Rest Mega Swampert suppoted by a cleric, and Diancie. And most of Diancie's viability comes from its ability to do just that: throw rocks on Entei while being a good Hydreigon check, with Heal Bell on top of it. I do not know how much Diancie's viability will change with Hydreigon gone but I am sure it will still retain an excellent niche due to Entei's presence alone. We have so many viable users of Stealth Rock, and not many of them appreciate Entei. While they can throw SR on other Pokémon, getting Entei in early can make sure it does massive damage before Rocks even become an issue.
Is Pursuit a good way of dealing with Entei, then? I do not think so. Neither Aerodactyl or Krookodile can come in for free against Entei. Aerodactyl's Pursuit does a pitiful 40%. Banded Krookodile fares better, doing at least 56%. That is, if Entei switches. If Stealth Rock are up, Entei will be at 75%. That means if it gets pursuited, it is not coming in again. Any and every user of Entei is aware of this. So you're playing a 50/50 here: is Entei staying on the Pursuit and burning you, or is it switching? Krookodile is one of the better offensive answers to Entei, but I reckon it is not because of Pursuit; I think the main selling factor here is Knock Off - which doesn't have many answers, either and has a decent chance to KO Entei after Rocks. However, that means Entei can switch out and return to be a terror (potentially because of Extremespeed) later on in the game.
Now to my last point, which would be Hydreigon: Hydreigon, in its Roost set, makes for a good Entei check on offense. Sacred Fire + Burn can still do up to 60% to it, making it possible for Entei to break through with Extremespeed / Flare Blitz next time (or stay in and get pp stalled), or for Hydreigon to fodder itself off by Dracoing Entei... which only has a 50% chance to OHKO Entei from full. If Hydreigon is choice-locked, it switches into Entei a grand total of once. That's not a bad accomplishment for an offense mon but Hydreigon is the biggest threat in the tier undoubtedly so wasting it like this is usually a bad compromise.
Sacred Fire will not always hit, being a 95% accuracy move. It will not always burn, the chance being 50%. However, you cannot play with this in mind; with such a high chance for great damage a burn, any player will have to consider these occuring and play accordingly. Entei has a very high reward vs any playstyle for very little risk and I find its flaws to be overexaggerated, the main one being Stealth Rock. Sure, the move is ubiquitous, but laying them down before Entei has already done its job is easier said than done. The same goes for forcing Entei out, especially without losing momentum and paving the way for a potential spin or defog. And yes, there are many offensive answers to Entei. Just the same, Entei can help against them as it possesses great priority. With so many great assets, I fail to see how Entei is not worthy of S Rank.
Edit: Forgot to mention SR Krook; until Entei knows its set (or it is the blatantly obvious rocker), it might try to play Purusit 50/50s so rocking on Entei itself takes a lot of guts. Krook itself does not want to switch into Entei.
