Just in case people haven't realised this, I'm almost 100% sure that there's a small quirk in the combo system which could have a decent effect on your score.
Basically, as far as I can tell, if you switch two Pokémon and make two matches at the same time, the one you moved with the stylus counts as the first in the chain, and the one that you switched with counts as the second in the chain - even though they actually move at the same time.
What this means is that if you're switching two Pokémon to make a match of three and a match of four, you need to be moving the Pokémon in the match of three so that the match of four counts second and you get more points for it than if you'd done it the other way round. Also, if you've got stronger Pokémon, you need to be moving the weaker Pokémon so that the stronger ones get a bigger boost by being second in the combo than the weaker one would.
This quirk also works in other areas. For example, if you've got two Pokémon with abilities, only the Pokémon you physically move will trigger, as far as I can tell. And if you've got a Pokémon evolved, it will trigger either before or after the other match you make at the same time depending on which of the Pokémon you are physically moving. This can have a pretty major effect in that sometimes you can be making two matches, but if you move the evolved Pokémon first it can cancel out the other match by making one of the parts of it disappear as part of its skill.
Anyway, that may or may not be helpful. It may not even be true, but I've played around a bit and I'm almost certain that it's the case.