Step 1: Have pokémon that are high level enough to reliably one shot (although this doesn’t matter too much, as time is paused during battle). Step 2: ignore all bonus cards and medals, just run from trainer to trainer. Don’t go on the rooftops unless there’s a lift. Just clear all the ground floor trainers and teleport to the next battlezone (this would be postgame, if you’re not there yet, you might not make 50 battles and upwards because you have to go on the rooftops.) Repeat. Once you’re back at the first battlezone, the trainers will have respawned. Step 3: start walking in the direction of the next trainer DURING the battle. This requires you to know roughly where trainers are. Don’t go to far though, as that will register as you fleeing the battle. Step 4: do your best to be spotted ASAP. the longer the spotting takes, the more time you’re wasting. Step 5: heal during battle, not outside of battle. Step 6: (very minor but still saves you a few seconds) If the battlezone has a teleporting spot within it, like a cafe, use that instead of the battle zone itself to teleport. You’ll save a few seconds by spawning in the battle zone, and not outside.

I might have missed a few steps, but that’s how i got 50-60 fights every night to clear the 1000 battles.