I seem to recall skyrim had a mod that guts out the whole dragon questline from the game. I haven't been interested it it, but it means to me some interesting potential for ttw and New California. One of the problems of compatibility is certainly lore, one does not normally have two childhoods and upbringings in two different vaults.
Your mileage may vary of course, but I'm not all that in love with the Fallout 3 dad storyline. I don't need it nearly as much as I'd love to see a tale of three wastelands. With the fallout 3 vault story and the dad re-jiggered or removed as appropriate, the capital wasteland simply becomes another place to visit and adventure - no lore conflict.
I've been looking into how it might be done myself, but it's above my head, and vault 101 has some very strange "spheres of invisibility" or whatever they are that hide huge areas of the vault, everything except for the people. The walls are still there, they're just invisible inside this weird invisible sphere. Makes it all the harder to tinker with it.
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