I think it's more because geomancer is such a broad kind of magic, and isn't really a single 'power'. Every mage has magic of one kind or another, and it always has a lot of varied uses. That's essentially what Raven is, an additional mage that travels with Emilia who has an exceptionally broad form of magic. As opposed to York who's a swordsman (and skeleton swordsman is awesomely cool), the 'magic' is as you said basically just showmanship and York's thing is swordsmanship at heart and any fancy sword moves he might have still fall under his swordmanship. Raven's is...lots of different tricks. Earthquakes, tornados, growing more powerful based on where he/she/it is, and whatever else might fall under geomancy. Er...is my point getting across? I ask because I tend to ramble and have trouble actually stating my point.
My basic point is that Raven (and a good guideline for future spirits Skeleton, Celestial, or otherwise) has multiple tricks or powers, which could step on someone's toes or keep someone from using a concept. It might be better to narrow their focus down, so that Emilia (and any other summoners) actually have a reason to acquire more spirits, to cover the failings of the ones they have. It's a motivator for them to go on adventure.
Good to see, having goals and ideas for story are essential for FFRPGs! And don't worry about being too much like Lucy, it's not bad to take inspiration from a canon character, or even someone else's character, as long as you put your own twists and personal touches on them. Emilia definitely is different from Lucy in my mind.
That said, if you do go the Skeleton Keys route (I like it just because of the name and implied imagery, I'll be completely honest >.>), I think there's some serious plot potential with how and why Emilia's keys and necromancy is different from the normal Silver Keys and Celestial Keys. Maybe someone, a long time ago, tried to create a new set of Celestial Keys but instead of using summoned creatures (which tend to have their own personalities which can interfere with using them (see Virgo and Leo to his previous summoner)), used the spirits of the dead to avoid getting any 'sass' from one's servants. For one reason or another though, the process went wrong/right(?) and created the Skeleton Keys!
...Or maybe Zeref made them, as he tends to make evilly looking things. With the stigma attached to them coming from using ANYTHING Zeref made, especially with everyone waiting for them to do something horrible.