Xerneas is an anagram of Serena with an "x" thrown in. It's more than likely unintentional, but to a Kingdom Hearts fan like me it's a hilarious coincidence.
So what would Serena's element and weapon be? Life and a version of Vanille's antler club from FF13 except fashioned after Xerneas's antlers? :P
Here's a real subtle one: I like how they allude, but never really confirmed, the Legendary Beast's having a connection with the first 3 Eeveelutions.
When the Brass Tower was burned down 3 Pokemon perished in the fire which Ho-Oh resurrected as the Legendary Beasts. While their types reflected the events which led the the tower burning down (the lighting that struck it, the fire which burned it, and the rain that put it out) it's also believed the 3 Pokemon that were resurrected were originally the original 3 Eeveelutions. Though never specifically confirmed, there are hints to this:
1. The Legendary Beast's Hidden Abilities are the same as the main Abilities of the original three Eeveelutions.
2. While not an exact 1:1, their roles via their stats are sort of the same (Raikou and Jolteon are speedy Special Attackers, Entei's and Flareon's highest stat is their Attack, and Suicune and Vaporeon stats can make them defensive Pokemon and Special Attackers).
3. Similarly you can make vague connections with their movepools. In addition to learning some of the same moves (which is obvious since they're the same type) Raikou & Jolteon learn a random Physical move that's not their type (Crunch for Raikou & Double Kick for Jolteon) and Entei & Flareon mainly learn Special moves but in this Gen got a highly wanted Physical move (Flare Blitz for Flareon and Sacred Fire for Entei (BTW Entei can't learn Flare Blitz)).
4. The Tower is in Ecruteak City which not only has the Kimono Dance Theater but also in Crystal, before going to the Bell Tower, you need to battle 3 Sages who all use Noctowl and, you guessed it, one member of the original Eeveelutions.