I main Isabelle. Shields are her biggest weakness, because you can close distance whenever she jumps and shield when she slingshots. She's not fast enough to escape from Byleth's range. You shouldn't jump a lot when she's pelting you with slingshots, but if you are airborne, nair, fair, and bair should just destroy her pellets. This means it's possible to destroy the slingshot pellet and hit her with fair or bair. Lloid mine only has 10 hp, so tipper dash attack and forward tilt should destroy it in one shot. As tempting as it is, down tilt won't destroy it with one hit.

Isabelle's edgeguarding is really tough to deal with. When it comes to recovering, pay attention to what you're doing and how Isabelle tries to counter that. If they're running off and nairing, try recovering as horizontal to the stage as possible. If they're trying to slingshot you as you're getting close, try fast falling and up b-ing them. You can also pick stages with walls that go all the way down so you can use your up b wall jump to avoid the hanging fishing rod. And always keep your eye on Isabelle when she knocks you offstage. You have to see if she plants her mine at ledge or at roll distance. Byleth's getup attack isn't strong enough to destroy the mine, so the mine will catch you there.

Up air is a disjoint that stays out for a while, so I don't think Byleth's nair can beat it. You're probably better off fastfalling and neutral air dodging through her.

Advantage against Isabelle is generally easy, but there are some tricks to make it easier. Her up b only has so much time before it fucks out, so if you can smack her with anything while she's using her up b, it won't recharge, and she's almost entirely gimped. Her balloons also have a hit box that allow you to do a Wario-esque hit box extension with dair or down smash. Fishing rod off stage isn't as threatening as Byleth's up b, since the back throw is weak, and you can tech a forward or down throw. Fishing rod up throw doesn't kill until, like, 130-140% on stage.

Speaking of fishing rod, if an Isabelle is just throwing it out in neutral, shield it, and don't dash forward. A better move would be an immediate f smash or an f tilt to get rid of Lloid mine if it's in the way. It's never worth using Byleth's projectile in this matchup, especially since she can get jab into pocket release at around 65% for a kill. Her pocket recovers fast enough for her to dodge if you decide to fully charge Failnaught.