This is quite the coincidence, I was actually wondering what in the world Eusis was supposed to mean after the name was mentioned in the Japanese/English name preference thread. Yushisu, to me, as someone who studies Hebrew and Greek, certainly looks like a possible Japanese approximation of the name Jesus. In Hebrew and Aramaic Jesus's name is, as Zio mentioned, cognate with Joshua's, and both appear as Yeshu'a and Yehoshu'a, respectively. Of note here is that in their original language these names are nearly identical, and share the "sh" sound.
But anyway, from what little I know of Japanese, I could easily imagine the name is an attempt at Jesus/Yeshu'a, but it may have some other meaning or derivation in Japanese. In any event, I do think it's possible some faint connotation was meant to be imbued to the character, maybe even something messianic. Remember that the vessel at the end of PS II (itself an ominous and perhaps ironically named one) is named Noah. Noah is seen as a prefigure of Jesus in Christianity, Gnosticism, and Islam, alongside the name's other apocalyptic connotations.
The problem is that, like Aeroprism pointed out, Christianity isn't as widely accepted in Japan, and there seems to me to be less scrutiny of the religion there. The popular culture there seems to love to throw around crazy Christian phraseology and ideas without really understanding them. I think a part of this is because in the Western world we tend to have, even if more passively, a closer relationship with Greek and Semitic culture and language, and thus sort of intuitively pick up on things in the religious culture that Japanese pop sensibility doesn't.
A good example to me is Neon Genesis Evangelion. The name is a grammatical mishmash and makes little sense from a structural standpoint. "Neon" is an adjective meaning new, in the neuter nominative singular, presumably modifying "Evangelion", or "good news/Gospel", and "Genesis" means "birth" in Greek (again in the nominative singular). So the title literally means "(New) Birth (Good News)" in Greek. Homer or Aristotle this is not. Admittedly, because Greek is a synthetic language grammatically and has extensive clarifying endings the structure is clear enough, but the language doesn't normally sandwich a noun with an adjective and accompanying modified noun in that way; apposition of this sort is pretty rare. In any event, the idea is clear enough, "Birth that is new good news", but, well, it doesn't look as exotic and alluring when you look at it that way.
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