Falcon/Ganondorf on one team may not be the most balanced or beneficial, but there simply isn't anything awesomer... although double Ganons is very close, heh. Admittedly, I've yet to play with Friendly Fire on in this game yet and that's a whole different game. A really fun game though that I used to play all the time in Brawl. As you well know Sykka, any time we'd get a match going on Fsmash it would be Friendly Fire on. Things haven't gotten too ridiculous with it off in For Glory though and a lot of the times I play with a team Ganon/Falcon it's with a friend against computers or other friends locally. That said, this has been an epic team I've loved since Melee.
Other than that pairing, I feel a Ganondorf/Palutena team would be fun just for the dichotomy of it.
Have yet to really experiment with 2v2 teams in this game, but I know Ray would say Robin from his own experience and I have to admit that Arc Fire into anything of Ganon's for guaranteed damage is a big deal. Likewise, Ness would be a good partner with PK Fire and other gimpy moves. Any character that has a move that allows a free hit for Ganon is a bonus... and all are capable of that but some leave much more significant windows.
For myself, I'm still fairly early in this game but I've always loved Falcon and I always try to make Samus work simply because I love the Metroid series so much. Link's been fun as well and is a character I always at least try to use. Samus and Link are interesting to use and require a mind set I often don't have the patience for. Link has good kill power now but Samus still leaves me with something to be desired. Gotta say I really like Zelda though. Something satisfying about using her now more than ever I'd say.
In terms of who is wise to secondary to cover bad matchups for Ganon. I imagine any "high tier" or "projectile user" would be good. Perhaps Rosa or Lucario. Not sure. Would have to actually play more... and actually seriously.