Hughes beat a young GSP but then GSP evolved and beat him. All sports evolve. For example, the most famous athlete of the early 20th century was a horse called Dan Patch after he broke the 2 minute mile trotting. People thought no one would ever do that again, yet now a days low level horses run faster than that every weekend. The same thing when the 4 minute mile record was broken by Roger Bannister or the 10 second 100 meter record - now a days, high school kids break those time barriers on the reg.
Not sure I would say Royce was not beating anyone either, as he did beat Ken who was a powerhouse in Pancrase. The truth is the sport was small, taboo, and underdeveloped back then and as time went by the talent pool increased and athletes just got better. Take nearly any well developed fighter from back then, and your modern fringe top 30 guy would maul on them. Who was the Ngannou or Jon Jones back then? There were none, just as there were no Tyson Fury type fighters back in the day. Primo Carnera was a giant back then but could not move or box to save his life, and compared to Tyson Fury he would be small, but Tyson moves like a middleweight.
All sports evolve, and it is no knock to point out the obvious.
But you're talking about the absolute beginnings of the sport. MMA is essentially a different sport from what Royce Gracie participated in. Pancrase was a different sport. Their records are just grandfathered in because there wasn't a hardline when MMA became MMA.
Ken Shamrock beat the crap out of Royce Gracie, it was just declared a draw because there were no judges because the UFC was bootleg back then. If you're talking about UFC 1, he did not even know Royce Gracie was a grappler and did not train for it. Regardless, saying Royce Gracie beat everyone around and then citing UFC 1 makes no sense, because UFC 1 was just an invite of several random martial artists - not some encompassing league of the World's Finest. Royce Gracie being the king of the barn was a marketing gimmick, it wasn't even remotely true.
If you're saying Hughes only beat GSP because GSP was young, then you could easily counter that and say GSP beat Hughes because he was old. Also, GSP being a better fighter than Hughes doesn't mean that he's only a better fighter because he came after. If Matt Hughes was born at the same time as GSP he would still not be a better fighter most likely.
You cite Primo Carnera (who was beaten many times), yet in the modern era you have Wilder who can't box to save his life either. Even worse was Nikolai Valuev. You could also argue that Ngannou has "no skill" as well, and he merely beats guys on physicality. Heavyweights seeing success due to their size is nothing new, and nothing that has stopped happening.
I'm not saying that sports do not evolve, but your examples are really not well thought out. You're comparing frontier days to modern days, instead of comparing an established era vs another established era. You would be surprised to see that even linear sports like athletics is still relatively close to each other - and you are seemingly ignoring that promoters change rules of their sports in order to give other athletes better stats (this happens in team sports as well).
Michael Jordan was an 80s basketball player, though some less knowledgeable fans seem to think was only a 90s player - do you think everyone in the NBA has "evolved" past Jordan? Or even the best players today? And he's a player that grew up with out the 3 point line for perspective in how old he is. Basketball is far more commercial and has more athletes, more sports science, more scouting, higher level of training than MMA (and some of those things than Boxing as well) yet it seems rather unconvincing that Jordan or even older players like Chamberlain and Abdul-Jabar would still not be among the best players if not the best in today's NBA. So why wouldn't that go true for boxing or MMA?
Boxing has been around forever, and the core mechanics of boxing have not changed much. Saying Usyk would beat Tyson because Usyk fought in a more modern era is just lazy, quite frankly.
Most all time greats lose to younger people because they're past their prime, not because someone "evolved" past them.