"It's just a video game." So why does any of this even matter to you when, as you say, it's "just a video game"? Why would Lightning crossing over with FFXIV bother you when it's just another fictional character in a video game's fictional world? If you can use this to pad your argument with someone defending a character they like, I can also use this towards you in regard to your concerns over story & crossovers.
You shouldn't worry about defending your position, because I mean, it's just a fictional story in video game involving fictional characters. It doesn't matter at all! :3