Interesting thought, but consider the engineering involved. An alien ship would have components of different shapes, sizes and configurations, despite the fact that all "ion engines" are massed at 10kt.
Consider trying to fit the engines from an Independence Day (the movie) fighter into an F-14. Yeah, the weight might not be a problem, but EVERYTHING else would be.
I think it's fine the way it is. Though I agree that if you do do an upgrade, the basic hull should remain unchanged, so you should keep the cool alien pic.
John