Goku decided to finish Janemba off, started to power up... then stopped when Janemba started doing some freaky stuff.
Assumatively, Goku wouldn't have fought Buu so much in the Movie 12 AU (I work it out to be between 2 weeks to 3 months later than the Buu saga) so he'd be more out of practice with his SSJ3 powerup, thus the intermediate-ness of SSJ2...
If you've already seen "Rebirth of Fusion" . . .
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