Most projectiles in general will give her a bad day. Especially the fast projectiles with decent flinch like Greninja's uncharged Water Shuriken. I love baiting the side B to send a fully charged one instead, tough. If she intercepts one of those via close range bWitch Time, the tiny damage output will result in almost negligible slowdown. And with SS to get out of the combos and a very fast aerial speed, and a reliable kill throw to finish the job, I can say Greninja can camp her quite safely. This should in teory work too for Toon Link, minus the aerial part, wich means you have to be carefull and use the F-throw if she gets too close. Remember, throws ignore B-Time, and either Forward or Back throws give you a good distance to fire more projectiles.
By the way, some disjointed hitboxes can hit her safely with proper spacing. Shulk's and Corrin's side Smash attacks are in general too long-ranged for Witch Time to reach the attacker, and some others like most swordfighters can potentially avoid the slowdown if you aim to hit her only with the very egde of the hitbox.