The plan is actually for her to be defeated by Ganondorf at a later time after resurrecting him, where he'll take over as the main antagonist.
Sounds too much like Cia... I'm sorry, but IMHO this "plot twist" is incredibly overused in the Zelda series, and in video games in general. Not that I'm shooting you down or anything, but I'm just saying, perhaps an alternative situation could be brainstormed...
I personally haven't played Hyrule Warriors so I can't say much about how similar it is to Cia, but yeah it's a common theme in the Zelda games. It doesn't matter much at this point as I'm not as concerned with the entire story until after I release a playable alpha with a full dungeon/boss.
This gives an idea on what I'm doing currently(though outdated and missing some details):
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I've also decided to have alternative evolutions like these:
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Those, for example, can be obtained by devolving your creatures and leveling them up holding an item.