Why do I want my character like this? Why don't I? Why do you play your character like you do?
I like her like this, I made her like this, yes, I could just go the easy way out and cave in to what everyone is telling me, but I wouldn't have fun playing her like that. I removes her individuality, it removes her conflicts, it means there is no damn reason for me to play her at all.
No, from where I'm standing, it
solves her conflicts. Indeed, makes her a bit of an "uber-character".
Your character has issues with getting submerged, a phobia of some sort. Her avoiding the wet-grave of a pod by controlling her ship like a conventional captain is
not avoiding the conflict. She sacrifices the efficiency of pod control because of her fears. That's cool, edgy and in tune with the spirit of the game. You contriving a super-pod that allows her to ignore that
is avoiding the conflict by nullifying its effects and trivializing its influence on your character's narrative. In fact, if you will do that, there is no point in making your character afraid of or incapable of using a pod, if she really won't be afraid of the pod at all.
Now, for another example to demonstrate what I mean, imagine that in a hypothetical Eve movie (or hell, book) you could start out with a character like that and have her overcome her fears towards the end to triumph over the baddies of the week. It might even be pretty interesting and compelling narrative. However, think about it. If in that movie our heroine just circumvents her fears with some technobabble gimmick at the convenient time it will feel pretty damn cheap, contrived and yes, Mary Sue-like to the viewers. The audience will boo, no matter how much the writer tries to tell us that the character is just so brilliant and how it really does make sense in the setting.
Alternatively, there could be a scene where the captain, her ship under fire and its hull buckling, walks over to the edge of the bridge that leads to the the capsule, looks at the dark liquid within and sees herself reflected, distorted all Funhouse-like. She's afraid, but to save her ship she has to take the plunge. She's deathly afraid, paralyzed even.
That's not contrived.
That's not skirting the issue.
Now you can come back to me to argue the circumstances of your character, how I got it wrong or how she's special, but I'm not talking about the specifics, nor even your character, but rather you-as-the-author and the principle of the thing.
That's addressing the conflict part and I see there's more to it... but
If you need a 'speshul' pod to retain her individuality, urdoinitrong.
Sardonic as that comment is, I do think that it somewhat covers the rest.