Id be happy if Vatti, and Agahnim team up tor revive gannon, and vatti not quite knowing what he getting him self into, It is ALttP so if gannon dont appear as a villain, the plot should at least be like AoL where they are trying to revive him and link aint having it cuz he just worked so hard to put him away.
Some People thing Agahnim IS gannon, which is fine, Vatti can Effe that up for him and he wont succeed makeing agahnim the main boss, which i think would be great, however your theory is on agahnim it can work, so maybe not bring gannon back considering its ALttP2 and Link just worked so hard to kill Gannon.
One think i would like to not is that link is still a child, so unless this is something that happen before the original ALttP, it makes no sense that he still look really young, you would think if it were a sequel to ALttP it would be later in time and he would be older, but that theory stuff dont matter to me as long as the game is good, i just thought i would bring it up!
it might be Ganon, explaining how and why he's alive in the 8-bit NES game.
He was never alive in AoL, Link stopped them from reviving him so he died in LoZ when he was Resurrected for the fourth time, (by timline standards) and he was finally killed in LoZ and has not returned since, so there is a chance Gannon will not be in Zelda 3DS unless its during LoZ or ALttP, or maybe after AoL, where Link prevented the resurrection of gannon, but soon after when he thought peace was established he let his guard down and Gannon was revived again after AoL. But as far as Gannon; hes been KILLED in 2 and 1/2 games (OoT with its split) so he is dead, Considering the cutscene at the end of WW in every timeline, so the only way to bring him back is during ALttP before AoL, or after AoL cuz Link only prevented the resurrection, not kept it from happening ever again.
So after SS and before TMC, being his first Cannon appearance timeline wise, or a continuance of the decline/link is defeated timeline would be the only way it would makes sense, even though they say Gannon is executed before TP but he make an appearance in it dont make sense, ill let that slide. but you get my drift, i feel im making sense, but you cant prove me wrong if you want