Ali 1967 was the best we all saw of him, but it's probably safe to assume he could have even been better 1968 through to 1970 had he not been unjustly stripped & banned from fighting.
I have a hard time picking against Ali '67, but a good few would have given him fits.
Frazier always gives him trouble & Smokin' Joe was also in his pomp in 1969 & Joe had the one punch Ali hated, the monster Left hook.
Larry Holmes, Evander Holyfield & Tyson '86 - '88 also ask a lot of questions of him & probably give him his hardest fights.
Lennox Lewis & Wladimir also had the size & skillset to trouble him, but I think they are slower than him & would have found Ali too fast & elusive.
Would also have loved to see how prime Ali would have handled Ken Norton's awkard style because Ali just never solved Norton, although, to be fair, Muhammad was not in prime the three times he fought Norton.
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