I'm quite bad at the battle factory too, but I get further when I take note of what moves the opposing pokemon have. So when you go to change you can switch out your weakest pokemon for a good one.
In your first pick get the ones with he highest stats and try and cover all the types. At least one defensive pokemon and 1-2 sweepers is good.
A ghost type comes in very handy to resist normal/fighting. Also make sure you have something that will beat Shedinja, either type advantage or status move like toxic.