I refer to the points made in the first and last part of the OP regarding why i left out Jon Jones.
I also think that several fighters on this list have beaten better competition while not being the naturally larger and longer guys and while not having had PED-*advantages*.
They're using cleaner transitions, better economy of movement, are typically more well rounded, and (from personal experience) specifically make a point out of being more technical because its necessary when you are out sized.
Look at DJ who fought the vast majority of his career with a glaring size disadvantage. He fought his way all the way to Cruz not because he was fast but because he was technical. He was able to overcome his disadvantages with cleaner technique and a more well rounded game.
Being small doesn't instantly make you better but or mean you have 0 physical advantages. But it does mean you gave far less room to be sloppy compared to MWs on up. That's why 145-170 have always been ridiculously stacked with the best talent
The reson those divisons are stacked is demographics, not talent requirements. Transitions and economy don't score in MMA, it's not gymnastics, and those things don't win fights alone, so what's the point in scoring them so highly in a GOAT debate?
I also disagree with these "physical advantages", being so exaggerated in bigger divisions. Holloway, cuts 25-30lbs, one of the biggest weight cutters in the UFC, has endless cardio and an iron chin (hasn't ever been knocked down, despite slugging it out all the time). These are all "physical advantages", some are related to size, some aren't. His chin and cardio are just as much of an advantage as Jones' reach and Francis' power. We saw how much this changed against Dustin, it was instantly obvious.
It wouldn't make sense for Francis to move like Cruz, it would be physically impossible and a waste of time and energy. He doesn't need to be as well rounded as DJ. It wouldn't make sense for him to spend time training gogoplatas, wheel kicks and having a 200 punch/round output. So to knock bigger guys down for not doing things that it doesn't make sense for them to do is nonsensical. Do we expect Max not to use his cardio or chin? The point of a sport is to use your advantages and gifts to the best of your ability and win within the ruleset, whether it's using skills, physicality, intelligence or a mix of all of them, I don't understand trying to judge it as something else.
Let me take this a bit further. Khabib was the most dominant grappler in the sport. A large part of why he had that skill was because he was born in the wrestling mecca of the world and was the son of a professional wrestling and sambo coach. So, Khabib's grappling skill had a component that was just as "innate" as Francis' power, Jones' reach, Max's cardio, etc. He didn't choose to be born in that context, it's his gift. Floyd is a similar case.
Other fighters can't match that experience whatever they do, just like you can't match Ngannou's power whatever you do. Now, why is one prized over the other? It's not like MMA is not a physical sport, why ignore physicality? Do we penalize Karelin for being "too strong"? I think this has to do with some romantic ideal about MMA being this purely cerebral/skill based spot, which is not the reality of it.
There's a lot of fighters with reach and height advantage (Struve, James Vick, Bigfoot, etc) that don't get anywhere near Jones' level. Same with power punchers (Manhoef, Hunt, Lewis, etc). So the argument to hold these things against successful fighters and turn a blind eye to their success, when others with the same advantages don't achieve anything great, is very weak in my opinion. Not to mention that many mental aspects like fight IQ, toughness, grit, etc, are just as innate as other physical gifts. I'm not sure why they're classified separately. Sonnen could never have DJ's fight IQ, no matter what he does.
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On a separate note, I don't really get the argument for not listing Jones at all. DC fought many notorious juicers with size advantages (Barnett, Bigfoot), yet Jones is the only one to outwrestle him at 205, and in his prime. Doing that to prime DC without high level credentials is simply insane and unprecedented, juice or no juice. Not to mention he dominated a division for a decade, we're talking complete and utter domination, including of other juiced fighters, and becoming the youngest champion in history, then holding that for record time.
The size argument goes back to what we talked about above. Holloway cuts just as much as Jon, and has an insane cardio and chin advantage, why not hold that against him too? Jon is also a notoriously weak puncher, yet found incredible success. Struve, James Vick, Brandon Thatch, Bigfoot, Sapp, Overeem, Lombard, Lesnar, Dillashaw, all either had huge size advantages and/or they were juiced to the gills, yet none of them ever came close to achieving what Jones achieved. I don't have him at #1, but to pretend Jones isn't a top 10 ever special talent is really absurd.