pato7 you need to finish the Charlotte quest to get Eva. You don't need Charlotte in your team or anything like that but there is the Ma Stone you get at the end of the Charlotte quest. If you don't have that Eva won't come out of the bottle.

I know this to be true because I tried to get eva and just got the key and when to fight her and she wouldn't come out of the bottle. I then had to fly back to where charlotte was and finish her quest. I got the Ma Stone and went back to Eva and all of a sudden she popped out of the bottle and I could fight her. Please get the Ma Stone before you do her quest. I wasted a lot of time and fuel with my mistake and I hope that doesn't happen to you.