I heard or read some where tht it was because of a rule. SSJ3 is meant to push the Super Saiyans power to it limits it should be more powerful or they should not have tht idea tht you can only stay SSJ3 for a short time. What they could have done in GT is tht Goku had to master SSJ3 like he did SSJ or tht he, like he need his tail to go SSJ4 but with SSJ3 you can fully unlock SSJ3 potenial and have no problems. 
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