Ganondorf's neutral is probably one of the worst in the game. He has a whopping 0 approach options. Ganondorf is one of the few matchups in which Robin can just spam Arcfire, because what is Ganondorf supposed to do? He can't run underneath it, considering he is the third slowest character and has one of the largest hurtboxes in the game. Should he jump over it, with that terrible jump height and third slowest air speed? And it's not just Robin; pretty much every character has the tools to prevent Ganondorf from approaching. Hell, at least Jigglypuff and Zelda can space aerials on shield. Ganondorf can't even do that, considering all of his aerials have a gross amount of landing lag and most of them take forever and a half to autocancel. And even for the ones that do autocancel, his terrible air speed means that most characters won't have a problem punishing him.
tl;dr Ganondorf has no approach options and is well deserving of his bottom 3 position, if not lower.
There's so much wrong with your own post. First off, Ganondorf doesn't need to approach against Robin's Arcfire, and if he has to, a perfectly timed Dash Attack gives Ganondorf just the low enough body to go under one. Often I will block Robin's Arcfire, but will tend to roll backwards just to avoid Robin's follow-ups, and if Robin throws another, I repeat.
Ganondorf can also jump over Arcfire, yeah, he can't truly approach like you say he can't, but he has his F-Air and D-Spec going for him against Arcfire after doing a second jump. The former is guaranteed to hit Robin if Arcfire whiffs.
And Ganondorf's aerials having a gross amount of landing lag may be somewhat of a reasonable argument, but his landing lag is actually better than someone like D3. Oh, and by the way, his Back Aerial and Up Aerial seem to have pretty decent spacing before they're auto-canceled, especially the former, which is a safe shield poke.
And besides, you're talking from the perspective of one character, a projectile character whom Ganondorf can just shield against to make the tomes run out. :D If you talked from the perspective of a character like DK and Bowser, Ganondorf actually has approach options against them. And you're also talking about one aspect of a character.
Pretty sure I've seen GanontheBeast just FHFFFair right over Arcfire. Fair and Bair are safe on shield approach options that need to be respected, though Ganon's mobility is a liability for sure. Zelda and D3 have decidedly worse approach options.
Ganondorf can FHDJ F-Air over Arcfire, I've done it before myself. His B-Air is a great shield approach option thanks to it auto canceling out of short hop, which is great to have.
You don't spam Arcfire really. Not with that frame data, not even against characters with terribad mobility like Ganon.
Also is there really a significant difference between the WiiU and 3DS metas (I wasn't even aware that the 3DS meta still lives)?
The 3DS meta is often "conjoined" with the Wii U meta despite having different stages that would be tournament legal and a completely different control setup and no margin for error. There are a lot of things you can do on the Wii U version of the game that you can't do on the 3DS version of the game, and some characters tend to be more viable or less viable in the 3DS game for these reasons.