I prefer the 101 startup (despite the fact that it's long). However, I thing there should be a choice, definitely. And on top of that a "Normal Start" and "Quick Start" option for Vault 101 (the former takes you through the childhood stages and the vault escape. The Latter just grows you to adult size, boots you to the front door and lets you pick all your crap, and lets you go through the vault 101 start without the hassle. If you go through this version you're also given random loot. Random crap, random amount of 9mms/ammo, random amount of clutter, random amount of clothes, etc. Plus a baseball bat, grognak, sweetroll, bobblehead, etc.) Not as much as if you did it "right", but not totally missing out either.)
And while we're at it, maybe some alternate starts too (both FO3 & FONV). Though this would probably be best served as a separate addon rather than a main part of the mod.
Ideally what should happen is something similar to what happens in FWE: You see the birth scene, are told this is either a dream of events far away, or the beginning of new life. It asks you if you wake up or live the dream. If you choose the former you get NV start/Alt start options. If you choose the later, you get FO3 start.)
While we're on this topic, I should bring up a semi-related issue. That being, that I noticed that several FONV-based mods don't' fire correctly until the FONV tutorial is done (just the part with doc Mitchell is necessary, not the stuff with sunny smiles), and likewise some FO3 Mods don't fire correctly unless the the FONV.
Seems what has to be done here is that once you complete vault 101 it should also complete the FONV tutorial, and then (if they keep it in) when you take the train to NV you're given a copied "fake" version of the tutorial.
Cause right now In order to make a new character and make all the mods I have work right (98% of which are NV based) I have to...
Only load TTW and a few other "essential"/safe mods (Project Nevada, XFO Two perks, Lings, And Skip DLC.) and play through vault 101 (that's what I hate about Beth games: such tedious intro dungeons. Yeah it's epic the first time, but after the 3rd time through it just becomes annoying.)
Coc to the CW train station and get a ticket.
Take the train to NV
Go through the NV Intro (which is thankfully short. even moreso in TTW.)
COC to the NV train station and get a ticket
Take the train back to the CW
COC Back to the Vault 101 exterior.
Save and exit
Reenable everything else.
Load all games.
Yeah it's annoying.
In the short term, what I would suggest is this:
Once Vault 101 is done, you don't get "following in his footsteps" (not yet.) Instead, you get a menu telling you to disable any non TTW tailored mods and save. It would then place a one-use teleporter at the exit of vault 101. It would work almost like the train switches but they wouldn't require tickets, and could only be used once. Also you would not get the "9 years later" screen. After that it disappear from the game completely.
Oh and an invisible wall prevents you from going anywhere else.
Then once you did the NV tutorial and step outside of Doc Mitchell's house, a box pops up telling you that it should be safe to reenable any other mods you have on you. asking whether you want to stay in NV or go back to the Capital Wasteland.
If you choose the former, you will not receive "Following in his footsteps" until you return to the Capital Wasteland (or better, you hear about james from some place.), and you will get "Back In the Saddle" like normal.
If you choose the latter, you are teleported back to the Capital Wasteland right outside of vault 101. (again, works like the train switch but no ticket and no cinematic.) and you do not get "back in the saddle" added to your pipboy. Instead you get that only if you walk into Goodsprings later on. In this case, "Following in his footsteps" starts up just like normal.
I know... it's not a lore friendly method, and not good storytelling. And it really doesn't solve the problem of choice, but it would at least be a short term solution until a better way to handle the intros are implemented.