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I would go with [name_m]Perseus[/name_m] because like you said, it has more options. Might depend on your last name though. If it’s something like [name_m]Smith[/name_m], I wouldn’t do [name_m]Perseus[/name_m].
I wouldn’t worry about the double S with [name_u]James[/name_u]. It sounds nice because it goes from 3 syllables to 1, plus you have PJ as a nickname option.
I’d probably just stick to [name_u]Percy[/name_u] but Perseu is great too! I think [name_m]Perseus[/name_m] [name_u]James[/name_u] sounds fine. Alternatively, [name_m]Perseus[/name_m] [name_m]Jacob[/name_m] could be a variation?
[name_m]Perseus[/name_m] [name_u]James[/name_u] seems best to me! [name_m]Perseus[/name_m] [name_m]Rodney[/name_m] does seem a little clunky but not too bad in my opinion! [name_m]Perseus[/name_m] [name_u]Spencer[/name_u] is a little too ‘s’ sound heavy for my taste.
Also I don’t think [name_m]Perseus[/name_m] is pretentious, but I might be biased as a PJO fan 
Unfortunately, [name_m]Perseus[/name_m] and [name_m]Percival[/name_m] come across as pretentious to me. I would stick to [name_u]Percy[/name_u].
I have two first names and I rarely go by both so I feel like it does make it more special.
I prefer [name_m]Perseus[/name_m] [name_u]James[/name_u] “[name_u]Percy[/name_u]”. It flows better in my opinion plus it does give him something else to fall back on as you said.
I adore [name_m]Perseus[/name_m]. Because of [name_u]Percy[/name_u] [name_m]Jackson[/name_m] I feel like most people know the story and won’t think “to destroy” so I don’t think that would be a problem.
If you don’t like [name_m]Perseus[/name_m], how about [name_m]Jasper[/name_m] (means “bringer of treasure”), [name_m]Pierre[/name_m], or [name_m]Pierce[/name_m].
[name_f]Hope[/name_f] this helps
@peach13 thank you! I get what you mean about the surname. Thank you so much! I was really worried about the flow.
@greyblue thank you so much for your input!
@bluecookies thank you! I agree about [name_m]Perseus[/name_m] [name_u]Spencer[/name_u] - I actually meant [name_m]Rodney[/name_m] suits [name_u]Spencer[/name_u] more (as in [name_u]Spencer[/name_u] [name_m]Rodney[/name_m] is one of my other combos!). Another PJO fan, fantastic! 
I never would have loved [name_u]Percy[/name_u] as much as I do if it wasn’t for [name_m]Riordan[/name_m].
@llewthewolf thank you for your opinion!
@emmalou23 thank you for your reassurance! I love [name_u]Percy[/name_u] too much to let it go, and I do adore [name_m]Perseus[/name_m] - I just wanted to make sure other people didn’t hate the combo!
I think [name_u]Percy[/name_u] is lovely!
If you prefer it as a nn then I like [name_m]Perseus[/name_m] and it sounds great with [name_u]James[/name_u], no issues having these two “s” ending names together
I like [name_m]Perseus[/name_m]! I think [name_m]Perseus[/name_m] [name_u]James[/name_u] works well, the S in [name_u]James[/name_u] is a bit softer so I dont see a problem with it.
Thank you both! It’s a relief to hear that