According to the Hyrule Historia, that's exactly the case. LTTP takes place in the timeline where the Hero of Time lost, thus leading to Ganon getting all pieces of the Triforce, the Imprisoning War, yadda yadda. Apparently, the Oracle games (where Ganon was "faux-revived") also take place after LTTP, then Awakening.
So, depending on where exactly "LTTP2" stands to take place in relation to all these other games, it wouldn't be totally out of place for Ganon to somehow come back into the picture. Twinrova almost accomplished it at the end of the Oracle games, so I guess anything goes in a world where prophecies come out of the woodwork and history has a knack for repeating itself.
But beyond all that...I miss fighting the Big Blue Boar. He's a hallmark of the series for me, and Zelda just hasn't been the same for me with him being second fiddle to Ganondorf.