The problem with "checking fighting-types" is that the only thing they have in common is their Flying weakness. Scraggy has a Psychic immunity, Riolu has Prankster, Mienfoo has a convenient movepool to get around its checks (aside from some Poison-types) so having a whole team to check them can backfire.
Oh, and Fletch possibly being S-Rank wouldn't just be because of Fighting-types. It also beats out all of the Grass/Bug pokes of the meta, as well as nearly any poke in the meta that doesn't have decent bulk. It in itself forces more defensive playstyles out of fear of getting OHKO'd/2HKO'd.
Flying is the biggest weakness for fighting types, so it's not surprising people use them for that purpose of countering fighting types Fletch doesn't really have more than taillow but priority.
Grass types and bug types aren't used is not really because of fletchling, is mostly because most of them either have really bad typing or inefficient for the actual metagame.
The metagame shifted against fletching and thus he's becoming more and more ineficient, it's not like some people will keep using fletching if everyone uses counters for it, because it sure has counters, it's not like any other pokemon that has been banned or ranked S, to be effective it mostly requires massive assistance from a team, and when it's a team work that is successful, i'm not sure you can really complain, it runs mostly the same sets. If it's one of the best gameplays there is , it's one of the best, but it's not uncounterable or even running totally unpredictable sets like other banned pokemon did.
Just because something broken checks another broken thing that doesn't mean it is healthy and should stay. Misdreavus is clearly unhealthy with its ability to bypass any of its checks, as well as outright limiting teambuilding. Mienfoo is clearly unhealthy in its prescence of just plain being the better choice to a lot of Pokemon. Fletching again forces teambuilding limitations, as well as even battling limitations. Fletchling forces so much pressure on a team to stay healthy, lest they just get outright swept with a priority acrobatics.
Misdreavus does have unpredictable sets, but he's also kind of fragile to switch into many pokemon, it's not like he threatens a 1HKO and forces you to switch you can mostly play around mind games with your opponent, but well, mind games also happen with other set up/sub mons.
Mienfoo has a very high MSS in my opinion. For the most he'll run drain punch, knock off, u-turn and fake-out/hjk/acro or even taunt, but he lacks ways to hurt fairy or poison types much, and flying types mostly force him to switch. Mienfoo niche is being a regenerator, but it's the kind of pokemon that really needs alot of support to be sucessful. It's effenciency comes mainly from being in a high speed tier and take a hit and u-turn, but nothing more. He's strong, that's for sure, but in no way overpowered or uncounterable.
Fletch doesn't exactly limit team building, if you run a rock/steel/electric type you can check him and counter him. If you have trouble with him, you'll have trouble with a tailow or a doduo, or even a vullaby for example. Fletch is a flying type that is overused because of priority, but that's the real only thing he has over other flying types, with fletchling gone, be sure you'll face the same trouble with other birds, that's pokemon.
Flying type are effectivelly strong against fighting types mostly because they don't fear their knock off like psychic types, while also outspeeding them.
