Simple answer, they do 2 different things for the most part. Emiya is mostly crit based and you'll find him better for taking on waves of enemies. Moriarty is much harder to work around but he's still very useful given you have the proper team. He can spam his NP and like Emiya crit very hard. So really it's up to personal preference, if you don't have the team or CEs to support Moriarty I'd recommend using Emiya just for the sake of easier use.
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