I've been playing TTW for a week or so now and really enjoying it. Had a thought while starting Broken Steel the other day. We know that Whitley works at Adams AFB from F:NV. A cool quest (unmarked most likely) could be to, while going through Adams with the CW BoS, you run across a non-hostile Enclave scientist (perhaps walking in on him just as he's sending the eyebot that will eventually become ED-E off on it's trip across the country) and can choose to murder him or let him live. Death items could be a note about the eyebot project.
Then, when we get to the Mojave, and finish ED-E's personal quest, there could be lines of dialog (easy to add dialog to ED-E by re-mixing its current beeps and boops) with ED-E explaining what the LW/Courier did with the enclave scientist back at Adams AFB.
Quest fail-states could be admitting to killing Wheatley - ED-E immediately becomes hostile and attacks, on death leaving nothing, or perhaps a pieces of encalve tech.
Leaving Whitley alive could result in an additional companion perk for ED-E, the LW/Courier having given it even more reasons to protect the PC now.
Either way, Wheatly should exit from the world map.
Continuity-wise, I think one could either disable ED-E in the Mojave until the completion of Broken Steel, or, if moving to the Mojave before Broken Steel, disabling Wheatley and having the PC miss the quest entirely when going back to do BS.
I'm more of a user of mods than a modder myself, though I am willing to help with writing and plotting if there's interest from someone well-versed in GECK-fu and NVEdit-jisu.