I've been playing Tale of Two Wastelands 2.8.1a, and on a technical level, the two games have been fused together rather well, bugs aside.
However, after going over the various Fallout 3 and New Vegas DLC and the main games, I had suggestions for a complementary mod integrating the two on a storyline level (installed optionally alongside the TTW mod):
Fallout 3 (stock): I'd leave some stronger ties to the Lonesome Road in Raven Rock. In Lonesome Road, we find out Colonel Autumn and his branch of the Enclave migrated East due to Eden's influence, and ED-E's storyline ties strongly into this, so some added holotapes should be added to Raven Rock with more information strongly establishing these ties. It would provide more reason for the Lone Wanderer to migrate west to investigate the source of the Enclave (and thus provide stronger storyline reasoning for the LW to eventually become the Courier).
Operation Anchorage: No changes.
Point Lookout: No changes.
Broken Steel: Edwards Air Force Base should have some holotapes and computer terminal records establishing links between Lonesome Road and Broken Steel (since it's likely ED-E's creator died when the BoS and the LW assaulted Edwards AFB). Also, after the destruction of Edwards AFB, their should be a more lore friendly way for the LW to migrate west (the train is nice, but not very immersion friendly).
The Pitt: Possible references to the Brotherhood out west (maybe even Fallout Tactics) could be added to Ashur's home in the Pitt.
Mothership Zeta: No changes.
Fallout New Vegas (stock): Nothing I can immediately consider.
Dead Money: The lines when the Courier and Elijah talk about the FEV could use minor adjustment's, with one of the Courier's text responses being something like "FEV....I think I've heard of that", and Elijah can go on as normal (this would play well to the Courier having amnesia yet establish they are the same as the LW).
Honest Hearts: No changes.
Old World Blues: No major changes, could have one of the Courier's text line responses when the Think Tank explain about your brain removal be something along the line of "This doesn't feel like the first time someone messed with my brain without telling me....", which would reference Point Lookout. (Doc Mitchell had good reason and explained himself adequately).
Lonesome Road: Some modifications to some of the Enclave records and the Courier's text lines could be made, the former to establish clearer ties with FO3, the latter to more firmly indicate the Courier is unsure how much Ulysses really knows (or if Ulysses isn't just making stuff up out of whole cloth), which would establish consistency with the Courier having an imperfect recollection of past events as established previous, not to mention throwing more doubt on if Ulysses is even speaking the truth about your past at all (if not outright making stuff up), which would resolve any immersion weirdness with the Courier being the LW.
Also, since it's established the Courier did settle in the Divide for awhile, records should be found on terminals/notes/holotapes with former Divide residents referencing how the Courier came there, settled down, mentioning of how the Courier once came to the Divide "looking for something" (clues to the origin of the Enclave from FO3), and decided to give up the search and just settle down for awhile.
I'm no great modder or storyline writer, the above is just my ideas for if anyone wishes to make a TTW complementary mod fixing any canon inconsistencies between FO3/FNV for the immersion nuts, and if anyone else has any other ideas, that's why I started this thread.
Note to TTW forum staff: I left this here in case anyone wants to undertake this in an official capacity as part of TTW (integrated into the main mod or as a complementary addon, but please relocate this thread to another subforum if it would be more appropriate there.