I vote for
Elisa. (I also like Elise/Elyse, but the a on the end does make it a little softer. Elysa could be nice, too, on that note.)
It seems like it's in between your other two options in style - feminine but a bit modern and energetic. I do prefer it to Elissa/Alyssa, which to me where I'm from is less classic and more dated.
I don't think it's confusing to pronounce (I'd say it eh-LEE-suh like
Lisa), and the nickname options are good:
Ellie,
Elle,
Lisa, Lis/Lise,
Lia?, Li/Lee.
Good luck! Let us know what you decide on!