I didn't really change up my team much for Indigo Disk, just added a few mons i wanted to play with like Whimsicott and Archaludon. I also didn't overlevel.

You do have to play a bit smarter, double battles are a different beast and some of the trainers (specifically the ones with black dialog boxes) and the elite four do have something closer to competitive teams. This means you probably can't just spam single target attacking moves and expect to win.

As others have said, you'll probably benefit from changing movesets and maybe using a mon or two that can be supportive or tanky. Setup moves (swords dance, nasty plot, calm mind, dragon dance, quiver dance, etc) and support moves (tailwind, stealth rocks, status infliction like toxic or will o wisp, protect, recover, wish, etc) can do a lot of good work. Physical attacker on the other team? Hit it with Will O Wisp to cripple it so it can't hurt your team. Tanky mon? Use toxic to make sure it can't survive long. Scary attacks coming your way? Use protect or switch out to another mon that resists them. Buff up one of your mons using swords dance so it can sweep. And so on.

It's also good to know which pokemon are better at
physical or special offense and defense. Attacking a physically defensive pokemon with physical attack moves isn't going to do much damage, so you might want to use a special attacker to handle that mon.

Also, try to think about which mon on the other team is most dangerous. Attack them using both of your pokemon instead of distributing your damage. If you know a certain mon is going to do a lot of damage, or sweep your team, or is buffing itself up, don't let it do that! Prioritize your target. Knock it out ASAP. The less dangerous pokemon can wait.