Team Flare turned out really different than what I was expecting. I remember when the leaks (as in, real photo evidence)started coming out, and one leaker on 4chan who was documenting all the important points in his play through, and then he got to the part where Flare's endgame was revealed: daining the life force out of all the Pokemon to power the ultimate weapon, and how everyone was going crazy over it cause, Team Flare was basically killing Pokemon. "***t just got real" was pretty much everyone's reaction to this. Personally, I thought I figured out their evil goal: Team Flare's twisted view of a "beautiful world", was actually killing off all the 'inferior' Pokemon in their eyes, possibly people too. And Megaevolutions could've worked in a goal like this. One of the requirements Team Flare would identify in a perfect, superior Pokemon would be their ability to megaevolve. This was where I saw the Nazi basis...but when I got the game, Team Flare didn't really strike me as Nazis. In honesty, they felt like they were more based off the fictional comic organization, League of Assassins. They even have similar goals. Maybe I wasn't thought fully in the goals and beliefs of the Nazis, but when I think of them, their familiar shtick of race superiority, etc. is what comes to my mind.
TL; DR: Team Flare=/=Nazis for me. They were more like the fictional comic organization, League of Assassins (and heck, Lysandre does have a hair style similar to al Ghul.) Future Gens I would like an evil team who's goal was something about superior Pokemon and whatnot. What do you want future evil teams to be like?
As odd as it may sound, I actually really liked the mechanic of corrupt/shadow Pokémon being captured from enemy trainers in Pokémon Colosseum/XD. I'd like to see that become a thing in a handheld version of the game.
In terms of what the "evil team" might actually do, I'd like to see some motivation based in time-travel, perhaps with the enemy capture of a Celebi or Dialga-like Pokémon involved to make the team successful (at least momentarily) in opening a rift between the past and present and attempting to alter the former to their benefit, perhaps even by leeching off of the successes and failures of other teams. Heck, it'd also make the perfect excuse to revisit modern versions of past regions and nostalgia-travel between the two.
EDIT: To clarify, I'd like that motivation to actually succeed to a degree that allowed player time travel.
"In the beginning, the Universe was created. This has made a lot of people very angry and been widely regarded as a bad move." -Douglas Adams