Question: Is it possible to use an element, in this case a ship, in a blender scene and progress through animation and then easily replace that ship with a different one? A replace command?

Answer: 
The best way to replace a "replace" button. :)

Create a proxy object that will be animated. Create as many ships as needed. naming them as object and mesh can be useful.
![enter image description here](https://i.stack.imgur.com/j30Bz.jpg)

change the mesh of the proxy object with another ship.

![enter image description here](https://i.stack.imgur.com/E1CTv.jpg)
![enter image description here](https://i.stack.imgur.com/zzLEY.jpg)
![enter image description here](https://i.stack.imgur.com/6DZuz.jpg)

The same animated object can be any ship you like with the same animation.

The resulting object is a linked duplicated, same as `Alt``D`. They share the same mesh. If you need an independant duplicate (same as `Shift``D`), press the button beside F (normally 2, counting objects sharing the same mesh) to make it a new object independent of the original. Use F button to give the mesh a fake user before changing it if you want it to be saved in the .blend even if no object use it (else it will disapear when you reload your .blend file).

![enter image description here](https://i.stack.imgur.com/ej2p6.jpg)
You can copy and paste keyframes in the *dope sheet* using `Ctrl`+`C`/`Ctrl`+`V`.

![enter image description here](https://i.stack.imgur.com/BfQa8.png)

This way you can animate one object, and then copy and paste the keyframes from that to any other objects.

Note (as [Greg Zaal mentioned](https://blender.stackexchange.com/questions/24455/can-i-replace-an-object-with-another-object-and-keep-animation/24458?noredirect=1#comment36050_24458) in the comments) that only objects with some kind of animation will show up in the dope sheet. A sort of mickey-mousey way to fix this would be to add a temporary keyframe to the object so that it will show up in the dope sheet, paste the new keyframes in from the other object, and delete the temp keyframe.