Akira nerfed everybody expect Goku (again). Goku has the Power of Plot to protect him in times of need. The show made it clear that while Goku SSJ3 was stronger than Fat Buu he's not tiers above him. Fat Buu's punches did little to harm Goku SSJ3 the same way Perfect Cell's punched did little against Teen Gohan SSJ2 who was roughly 100 times stronger than Cell was. So Goku at SSJ3 was probably 50-100 times stronger than Fat Buu, judging how the fight went on. Goku did however said that a figther stronger than him would appear to fight him, now Goku could have exaggerated about that just to get Fat Buu's blood flowing. Still Gotenks SSJ would have been enough to take Fat Buu on witch makes Gotenks SSJ in the SSJ3 tier, more or less. However if you add SSJ2 and eventually SSJ3 Gotenks to the mix than Goku quickly gets overshadowed by the fused warrior because adding the multipiers off SSJ2 and SSJ3, would make Gotenks SSJ3 500 times stronger than he was before, more than enough to overpower both Fat Buu and Goku SSJ3 at the same time.
A couple of new enemies appear like, Super Buu, Buutenks and Mystic Buu. If you compare those fighters with Goku then Goku should just sit on the bench because he's up against opponents who are hundred times stronger that himself..... and the fans won't have that. Goku is the main star of DBZ and you can't have the main star of the show to sit on the side lines for 50+ episodes can you, so Goku ivokes the Power of Plot and manages to tank hits from Buutenks and later in his SSJ2 form no less, takes hits from Mythic Buu. The...F! yeah Mythic Buu was pretty pissed when Vegeta SSJ2 rushed him and he really showd that he wasn't playing around and gave Vegeta some HARD hits, same for Goku SSJ2... but both Vegeta and Goku stood up from that and where ready to fight some more...... now.... this is ridicilous. Mythic Buu... is really really strong, he's easily a couple of 100 times stronger than Goku SSJ3.... but.... Goku/Vegeta where in there SSJ2 form to begin with.... yeah. Remember when Gohan nearly comatosed Cell with just 2 punches? yeah a pissed off Mythic Buu who's miles ahead of a bunch of SSJ2's would punch there heads off with his pinky.
Goku got a Zenkai boost from Akira when nobody was watching so that Goku isn't the Raditz of the group. I know that the movies aren't canon but the movies show what Akira thinks of the rest of his characters. Its always Goku who saves the day. Freaking Hirudegarn was so damn strong that he was able to ONESHOT Gotenks SSJ3 and beat the ever living crap out of Mysthic Gohan, both of them are stronger than Goku was. Yes here comes Goku taking DIRECT hits from the Godzilla monster like a boss and out of nowhere activated a hax attack and finishes a monster off who moments ago solo'd the Z Figthers like nothing.
In the beginning we got a strong sense that Gotenks SSJ would have supassed Goku SSJ3 nevermind Gotenks at SSJ3, but Akira doesn't care for consistencies like most writers do and buffs Goku up to the likes of Mythic Gohan. Screw that.