Teach your Braixen Fire Pledge from the Move Tutor in Lapis Ward, and you can use it to burn Shelly's Forest Field, turning it into a Burning Field. It will stop giving her Pokemon boosts, while boosting the power of your Fire moves.
Also, when Yanmega comes out, you might want to try paralyzing it with Spark's high chance of paralysis, as it will become less of a threat then.
That's pretty much all of the advice I can really give, since Shelly becomes much easier once her Field turns into a Burning Field.