Well sometimes people assume I'm calling them an idiot, which I'm not trying to do. You may be missing a model or a texture, I'd say try redownloading it.
I think this sounds like a pretty cool idea, bit far-reaching but I think with the right amount of help you'd do a great job. I'd offer what little help I could give but alas I am a little tied up in trying (and failing) to design my website right now, I'll be keeping an eye out for the mod though, and if you want to bounce ideas around I'm on here most everyday.
For realism you may want to check out either Arwens Realism Tweaks or FWE. For textures it really depends what you want, just browse through the categories on the nexus.
May I ask why you would need such a tool? Al the modding for fallout 3 is done in the G.E.C.K, the only reason you need to edit an ini file is for Archive Invalidated, and there's a program for that.
For your last two questions: You should get FOMM, FOSE, and maybe FO3edit. No, the skeleton they use in fallout 3 is different from oblivion, so you can tweak the models a bit but not directly add to your esp list.