It's likely N didn't challenge any gyms, given the gigantic stink he raised about the ethics of pokemon battles and that until getting a legendary he never really carried any pokemon (in all the fights with him, the pokemon were from the surrounding area, meaning they were catch & release).
Given his goal was less "become Champion" and more "defeat the current Champion with a symbolic legendary dragon" he probably faced the elite four and Alder in a unorthodox unofficial match, and he got there via force with Final Fantasy VI's burrowing castle. The elite four probably got in his way in an attempt to soften N up for Alder, to no avail. N's victory was likely never going to be officially recorded, but N/Plasma didn't need it to be since it was just the act itself that mattered. Either that or his entire fight was invalidated because he did kind of hold the place hostage. That couldn't have been legal...
Plus he used a legendary in a Elite Four challenge like a scrub! We don't want no scrub! (a scrub is a trainer that can't get no E-X-P)
You the player had to do things legit since you are supposed to prove that the current system works as-is. If you skipped gyms or burrowed your way to Alder then you'd be proving that there's something messed up about the pokemon league, proving N correct. Sorta.
One question I always had was where N's other pokemon came from (Zoroark, gearface, ice-cream, and the two Unova fossils) despite his extreme displeasure of raising pokemon. I mean, the game reason was to give us a full fight of course, but what about plot-wise? The Zoroark could be related to the one in the intro-cutscene (and was raised with N), but I think the other four could have been revived/created on the spot by Ghetsis so N would have a full team for the elite four. At least that works for the fossils and maybe Klingklang. Maybe N went to Dairy Queen and willed his sundae to life?
Actually, I like the idea that Ghetsis set N's team up, since despite being a strong team, N's final team has a BIG fighting weakness, so Ghetsis might have helped him arrange his team with the intention of destroying them once N served his purpose. This theory would be cooler if Ghetsis actually used a fighting-type in B/W but I digress (he does have focus blast on his star-mon at least).
But Shauntal and Grimsley sound like they don't know N's intentions, Shauntal just sensing there's some kind of hidden sadness while Grimsley was surprised there's a second challenger so soon (though considering Cheren came with Alder in the "final" cutscene of the main story it could be that Cheren was also battling his way through the Pokemon League and as it happened your paths just never crossed). I suppose they could have been pretending nothing was wrong for the sake of not worrying kids though if that was the case you'd think they would also know we're the kid involved in all this (or were they not paying attention and/or Alder/Marhshal not tell them?). It honestly seems like they just assumed that since N is challenging them that he must have gotten cleared by the Badge checker (and/or assumed if the trainer really wasn't strong enough they'd just beat them anyway; if anything the Badges are sort of used as a way to prove the trainer has trained enough to be able to challenge the Elite Four. N sort of cheated by using a high leveled Legendary Dragon to force his way through).
Hey, if the game gives you a Legendary before the League than its fair game. Heck in ORAS they're practically begging you to use Lati@s.
Well the Zorua we see in the picture is a different Pokemon than the Zoroark that N uses to battle since we get the Zorua and Zoroark remains as N's bodyguard. If I had to guess the Pokemon that N use in the final battle are strong abandoned Pokemon (how else would he have gotten the Fossil Pokemon unless they were abandoned, I'd imagine N would be against reviving extinct Pokemon) or were strong wild Pokemon negatively affected by people in someway. Oddly the Pokemon in N's final team are the only N Pokemon you don't get in BW2 (which makes sense for Zoroark, but what about the other's?).
I think someone did point out that N's entire team, including his dragon, is weak to something Hydreigon carries, even before you look at the rest of his team's match up. The only ones with a chance are Zoroark and Archeops by outspeeding, though Zoroark is the only one with a SE move in Focus Blast. Oddly enough it would also be the only one Ghetsis didn't orchestrate N having for the battle in this theory.
Not just Hydreigon. Ghetsis entire team seems to be built around to taking down anything that N could use against him as
Mew King said:
Zekrom/Reshiram: Seismitoad shouldn't have that difficult time tanking their elemental STAB and hitting them with a Super Effective STAB of its own. Hydreigon has Dragon Pulse as well (and oddly N's dragon doesn't have a Dragon-type move). Also only Reshiram has a move that at least one of Ghetsis Pokemon isn't immune to and its Fusion Flare which is resisted by Seismitoad and Hydreigon.
Carracosta: Eelektross got that covered, and if not him then either Bouffalant (Wild Charge and Earthquake), Seismitoad (Earthquake), or Hydriegon (Focus Blast).
Vanilluxe: If Bisharp doesn't take it out with a Stone Edge many of Ghetsis other Pokemon have a Fire-type attack waiting like Eelektross and, of course, Hydreigon.
Archeops: Once again a good Electric-type attack (or Bisharp's Stone Edge) would at least bring it down below half.
Zoroark: Bisharp is packing X-Scissor, and Hydreigon has Focu Blast.
Klinklang: I've pointed out the Fire- and Fighting-type moves that Ghetsis' team has.
Only member of Ghetsis team who doesn't directly have a role against N is Cofagrigus though from the looks of its moveset its more meant to stall and slowly weaken so maybe one of Ghetsis other Pokemon could be sent in to clean up. In addition N's team doesn't really have a lot of ways of defending or countering against Ghetsis team. So whether Ghetsis helped him pick out the Pokemon that he did or just knew the Pokemon that N would have on him, Ghetsis did look like he planned his team around beating N's.
And being Seismitoad's Ability is Swift Swim and it's carrying Rain Dance, if Speed becomes an issue looks like Ghetsis prepared for that.