I think you should do what you think will make the best mod, and what will be the easiest/most practical to work on. Personally I think that would something along the lines of what I was saying in the WMX thread (though obviously I'm biased), since once it's set up it would be a (relative) snap to add support for things like WME and WMX in compatibility patches; just a matter of adding things to a formlist. By the same token, it would make future expansions to the mod itself a lot easier.
Incidentally - and you may already know this stuff - if you do take that route, make sure the formlist has 'OrderedList' at the end of its EditorID so that FNVEdit knows to not change the order of items in it when making an automatic merged patch. Also, when adding items to an ordered list in a compatibility patch, you need to add the new items at the bottom of the list (again so that FNVEdit's merging will work properly). Annoyingly, the GECK adds items at the top of formlists when you drag and drop, so it might be easier to use FNVEdit for this.