H-here I go...
Give the Team Flare scientists some actual personality. Also, AZ shows up a couple more times before the Team Flare shit hits the fan, so he doesn't feel like he came out of no where.
After Lysandre calls you in the Holo Caster and tells you he's going to go Hitler on the world, you can go talk to the NPCs, and they'll have varying reactions. Some will freak the fuck out, while others will think he's just bullshitting or it's a prank.
At the lab, you only fight one scientist, and when you reach the end, there's no "LOL PRESS A BUTTON!!! :D" bullshit, you just get there too late and then you see the cannon rise.
Once you arrive at the HQ, Lysandre doesn't battle you quite yet. He does his little motive rant, and then starts heading towards the legendary, having his grunts gang up on you. As you progress through the HQ, instead of fighting a bunch of nameless admins, you fight the other three scientists. Once you get to the legendary, Lysandre is there, about to activate the cannon. Shauna and Serena attack him to get him to stop, while you have to release the legendary from the machine. Unfortunately, doing so awakens the legendary, and it attacks you. Commence battle.
After you deal with the legendary, you see that your friends just got their asses kicked, and Lysandre's pretty booty blistered that you fucked up his plans, and attacks you. After that, the whole situation just goes the same way it did in the actual game.
When Sycamore talks to you about Lysandre, he goes into a bit more detail about it, clearly showing he's rather upset about the whole thing.
Also, gym leaders would actually do shit besides being a gym leader, sort of like in BW1. Viola, Korrina, and Wulfric were the only ones who left their gyms. I'm not crazy familiar with X/Y's plot so I can't really come up with things for them to do, but I'm just throwing that out there.
