Small one, but, here we go. I know some people might find it a bit confusing why Lysandre uses a Gyarados as his ace. I believe it's because both are harbingers of destruction. Gyarados is Gyarados and is known for its violent and destructive tendencies. Lysandre wants to destroy most humans and all Pokemon. So yeah, they fit each other in that regard. I could be wrong though, speaking that X and Y are some of the least thought out games in the franchise.
Lysandre's team is odd in general as, aside from his Pyroar, it doesn't feel like it quite matches him:
1. One main think working against it is that he only has four Pokemon. Maybe if he had a full party and they were all different Types it wouldn't look so odd, but as it stands now the Mienshao stands out and the Gyarados is odd being his ace.
2. Speaking of his ace, while I understand they wanted to give him a Mega Pokemon as his ace, still his design is partly based on Pyroar. It should be equal level to his Gyarados. Also Mega Gyarados is an alright Mega for Lysandre, as said representing his destructive goal. Kind of wish they did what the anime did and gave him a Shiny Gyarados, infact making his team primarily red/orange color would have been a theme that made some sense.
3. Another idea is that they could have made his team to counter the Legendary Pokemon. Seriously, aside from Pyroar all his other Pokemon are weak to Fairy-types (and his Mienshao is also weak to Flying so no matter what the Legendary it's going to go down easily)!
This is, in my opinion, a stark contrast from Ghetsis's team in BW. Actually, I think what I'm about to say can count as a theory so:
NEW THEORY: While at first it also looks like his team is a bit random, if you look at Ghetsis's team in one aspect it's probably one of the best teams made by a villain team boss: Ghetsis's Pokemon were specifically chosen to be counter to N's Pokemon:
N's Pokemon: Ghetsis's Counters:
Reshiram/Zekrom: In addition to Hydreigon, Bouffalant & Seismitoad have Earthquake, and Bisharp has Stone Edge for Reshiram.
Carracosta: In addition to Eelektross and his Pokemon that know Earthquake, Bouffalant also knows Wild Charge and Hyreigon knows Focus Blast.
Vanilluxe: Bisharp has Stone Edge (oddly it's only Steel-type move is Metal Burst), Eelektross has Flamethrower, and Hydreigon has both Fire Blast and Focus Blast.
Archeops: Eelektross, Bouffalant w/ Wild Charge, Bisharp w/ Stone Edge, and finally Seismitoad (& Hydreigon knows Surf).
Zoroark: Bisharp has X-Scissor and Hydreigon still has Focus Blast.
Klinklang: Hydreigon w/ Focus Blast, Eelektross w/ Flamethrower, and Bouffalant & Seismitoad w/ Earthquake.
And yes, Ghetsis's Hyreigon can counter ALL of N's Pokemon. Not to mention he first sends out a Cofagrigus who Toxic Stalls (and any Physical attacker gets their Ability changed to Mummy). Ghetsis's team is laser focused on defeating N's team. A very nice attention to detail while also giving him a well-rounded team just in general.
In B2W2 his team becomes much more of a team a villain would have, swapping out Bisharp and Bouffalant for a Drapion and Toxicroak. However the notable thing for that team is what they did with Hydreigon: they gave it max power Frustration and its holding a Life Orb. You know, just in case you thought Ghetsis may have treated his Pokemon any better then his adopted son.
Now that I think about it, I could ask the same question about your rival's Mega Absol in the postgame. Really, Diantha's Gardevoir is the only one of the four Megas you face in XY that makes sense from a theme standpoint, because even though Korrina's whole family supposedly had Lucario back in the day, Lucario still doesn't match Korrina's personality in my eyes. She seems more like a happy go lucky person, which isn't what I think of when I see Lucario in, say, its own movie.
Considering the Mega Pokemon available the choices for the Rival's and Korrina's Mega Pokemon feel fine. Honestly I don't know if there's any Fighting-type that matches Korrina, she's a bit of an oddity when it comes to Fighting-type experts as she doesn't study a martial arts but rather is just a very athletic roller skater.