Interesting point of view!

My main gripe with your solution of using Nodes and references (be them references or entity reference or whatever) is the unecessary overhead that is generated.

Node have revisions and other properties (sticky, promoted, published) that simply may not apply if you just want a user-editable list of values.

Maybe dumming down the taxonomy module and moving some of those assumptions to a separate module would be a more feasible solution?