ANY (technical) reason behind submitting sequences to GenBank versus ENA Sequence
Opinion: I prefer to use EBI/ENA because the turnaround time for "customer service" on editing metadata about a submission is faster than on NCBI. Inquiries to change metadata on NCBI can go unanswered for up to six months in my experience.

Answer to your question: No, there are no technical reasons that make it preferable to submit data through one website or the other. All entries end up being hosted by both databases anyway. The preference is up to the user to select whichever upload interface they prefer.