I feel that ponyta possesses most the qualities to rival pawniard and mienfoo at S rank. Most the time when a random little cup player asks for critiques for his team I end up telling them that it's "kind of ponyta weak". Sure there is a lot of fighting weak, foongus weak, fletch weak, abra weak, and pawniard weak teams but ponyta is probably the most common weakness I see in teams. Like they might have one thing ponyta won't want to be matched against like chinchou but once that's dead the whole team is vulnerable to burns, fire type damage, and that sexy speed tier. The best counter for ponyta is awkwardly ponyta itself. Diglet, on the other hand, is definitely the best check, but it's not significant enough to diminish all the amazing potential behind ponyta.
Probably the best thing about ponyta is the the simple threat flame body creates in the use of physical moves (most notably u-turn). Fire types are uncommon in little cup and physical attackers are more predominant than special attackers in this meta which further boosts the value of burns. Spritzee is the most common status remover for those burns but as we all know it matches up poorly vs ponyta. In a way, ponyta is a nice answer to the spritzee/ferroseed core we see on many teams. Now that missy has left, IIRC ponyta now has the highest BST in little cup at 410.
Ultimately, the weakness to stealthrocks opposed to the resistance to it we see in mienfoo and pawniard is probably what holds back ponyta the most. Even with the threat of flame body hax, once ponytas eviolite is knocked off it's significantly easier to take down. Guts Timbur vs ponyta is often a close match up since 2 flare blitz can potentially take timburr out but guts boosted drain punches also take a lot out of ponyta. The combination of Stealth rocks damage and flare blitz recoil can often bring ponyta into a range where something on the opponents team can take it out.
Ponyta is the best fire type and plays a powerful role in LC. It deserves more usage than the ~10% it has compare to mienfoo/pawniards/etc, but ponyta doesn't quite possess the qualities to move up to S rank IMO. Besides the weaknesses to rocks and recoil damage there are other inconveniences for our fire horsey. It will never have the potential to check anything that shell smashers, it is weak to aqua jet, and as I said diglet is an deadly trapper for it.