Just a few observations and suggestions - this is so cool!
Depending on how integrated this is to blender? If you make this addon so it will build the FBX information; and then the export process would be the same from that point on… as a consequence the FBX2UE4 pipeline could then work for any tool - that is you could use the exactly same pipeline in all other tools that can build FBX and somehow run Python! Say - you could, in theory, do this in/from **Makehuman **and Houdini… as-is, with only a few modifications!? (Makehuman already links directly to blender, but it would be neat if you can do this directly from any tool… using Python of by the FBX format… for now Blender could however serve as a “transition tool” you import from any of the other tools, and transfer it to UE4, you would probably use a specific script/addon for each tool that.
For the design part. You need to move the export option away from the preferences and to it’s own tool-tab - this demo session clearly demonstrates that you need that?
Also you should be able to have different preset-set transfer options. Perhaps it could be done in a clever way… say when you change an animation and the shape keys… then the corresponding UE4 options gets set and done automatically!
**For the transfer **it looks like you can transfer one mesh “object” only? Would be possible to for us to have more collections and then export one or more… say you want a character, props and cloth in separate collections…
**Metadata, Versions and source control… **messing with Blender/UE4 quickly leads to problems - you got the FBX reference but where is the original blender files etc. Would it be possible to add meta-data to the UE4 assets, or to the blender files - or perhaps even better would it be possible to save/store the blender files etc. as part of the UE4 project, and to link it all source control.
This leads to something missing in Blender: a better way to organize your assets. I suggest that there could be a (Blender) project structure that “match” what we have in UE4. Say, you could build a collection set that match 1:1 the folders you have in UE4… in that way there would be a better correspondence between assets in different tools - that is: we don’t have to remember that! Say when you import the asset to Blender you can keep track of the source in a Blender2UE4 project file. (For starter you can store the sources in the UE4 project folders… )
Blender Question - I had to learn that the shape keys are broken by some modifiers (it is not obvious what happens and there are no warnings, they simply don’t get imported?), will the tool somehow be able to get past that, could it simply give warnings or perhaps simply “bypass” modifiers that wont work for UE4.
(Edit: I know this is not part of this FBX pipeline, but it would be very cool I I could make huge tiled height-maps in Blender, and then export them in the UE4 format. Probably not a huge task to do this - only I don’t know that much Python yet. )
Really Epic, you didnt have to, christmas was just month ago 
… why not use the new open source Pixar USD format? The industry seems to be heading that way.