Tales of Legendia/WMG

Senel is an AU Hugo
If he really did anything with Shirley, it confirms him as a Memetic Molester. Combine that with the fact that if you picture Shirley with black hair, her overworld sprite would look very similar to Marian's. Something's up here.

Chloe uses a prototype of the Alvein style of swordsmanship
Think about it. The Alvein style is commonly seen as being sword moves plus kick techs. Chloe is the first Tales character to start using kicks for moves like Tiger Blade rather than traditional slashes. Seems to me that she's experimenting with the two different kinds of fighting style. Perhaps she picks up some more moves from Senel to complete it post-game? Since the Eternal Sword exists in the Aselia and Legendia 'verses, who's to say there can't be travel between the two?

The Sacred Eres were going to be the game's Mystic Artes
Pretty much self-explanatory, and a valid reason as to why you'd want them (ie: they're crazy powerful, after all) but the actual moves themselves got cut from the game due to time constraints. Once they're obtained, everyone gets stat boosts when entering Climax Mode at least.
 * Interestingly, I think Holystar has found unused voice clips that suggest they might have had Mystic Artes. Maybe they decided to implement them in Tales of the world: Radiant Mythology 3 since Senel, Will, Norma, and Jay appear and have Mystic Artes.

Grune and Schwartz are the God of the Tales (series) multiverse
They're just split into two, one good (Grune) and one evil (Schwartz) and the summon spirits are Grune's servants. I think it's unknown who really serves Schwartz other than the black mist.

The legacy is a ship from Fodora that escaped from the planet's apocalypse
It's a common science-fiction scenario, a spaceship that can support thousands or millions of people escapes the planet before a cataclysmic event happens. The Legacy uses the Merines as a power source because it was originally meant to use Lambda instead. However; they couldn't get their hands Lambda because of the conflicting factions (including Emeraude) so they had to use a different and more finite power source. Whatever power source they had only got them to the world in Tales of Legendia since it had a breathable atmosphere but upon landing there, found that it was an Ocean Planet and had to terraform it. It was then that they discovered a new power source that was actually compatible with their devices that they intended to be used for Lambda...The Merines. Specifically, the Merines because s/he was sort of a Demi-lambda, so they used her to terraform the planet and make it habitable. Eventually, they spread out onto the land and became the "Oerines" as the Ferines called them, and as time marched on and on, forgot all about who they once were and didn't keep circulating the tapes and stories about their homeland. When the Fodorans, now Oerines, forgot that they were originally Fodorans and continued to oppress the native Ferines, the Ferines eventually struck back and took control of the Legacy and attempted to use the machinery their ancestors built against them - remember nobody remembers this because like with the Pern series, they all forgot that they were really aliens. This made the twist effective. However, meanwhile on Fodora...