It would have been bad storytelling to Let him use God whenever.
Thats why he never used Slifer til the finals, where all his opponents had access to something comparable. it would be a complete Drama kill. as for the Dark Magician, it was merely "his rarest card" for a long while. It wasn't til like halfway through did the Magician have any real significance. and once he had all 3 Gods, he lost access to them (in the anime) or there were no more Card games (in the manga).
and I wouldn't call Atem's deck the weakest, don't forget Archetypes were not a thing at the time, every deck was Your40best/favoitecards.dek. Hell the fact it DIDN'T depend on some card or combo like most other characters is what made it the so good in-universe.
if we had to call someones decks the weakest, it would be Yuma (completely dependant on 1 monster and Zexal ex Machina-related stuff to support it, Go first set Solemn, GG) or Jaden (Loads of incredibly situational cards and a very resource draining Strategy, think about how well Jaden would have done if Pot of Greed was banned in-universe too)
Yusei had the best, no question, as...well he simply had the most Extra. he didn't rely on Bullshit like Yuma, situational cards like Jaden and had other monsters he can fall back on if Stardust wouldn't do the job.
Yuya is shaping to be a nice runner up as he is getting more and more flexible.
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