Vault 101 should be the only place to start, but I guess whether or not it's the best plan for the most people isn't entirely certain.
We have to decide whether we're making a mod that allows people playing New Vegas to screw around in Fallout 3 for fun and added replayability, or a mod that attempts to merge the two games into one. If we're going with the former, I think we should do the "choose your start" method with the in-game window. If we're going with the merge, we should make Vault 101 the only choice.
I see this as similar to other balance/design decisions we have to make, like balancing between the games and crossover and such. Fallout 3 start is the only beginning coherent with the story, and we should only make it a decision if we absolutely have to or if our goal is to just have Fallout 3 as a side adventure.
I'm against even having an option to start in New Vegas, but if you all insist, then I would recommend that the New Vegas start automatically completes the Fallout 3 main quest, as if someone else did it. That might take some effort to work out, but at least that would make some sense. If we did that, players who want Fallout 3 as like another New Vegas DLC can have it like that.