well, how would we have obtained our Personas? While it might be quicker to have people start with their Personas, is there any way to find out who has the potential and who doesn't?
An alternative idea is that everyone has awakened to their Persona abilities, and initially have to get in contact with the other Persona users. In numbers lies strength, after all.
More importantly, though, is how will the issue of relationships be managed? Things like that take time and money, and thus we probably need to roleplay it day-by-day, with the GM deciding when to start a day or end it, and when does the "Dark Hour" open.
Some things would need money, so while it's best to abstract money (i.e. just run it without numbers), GM permission would be necessary for certain things - driver's license, buying a bike/used car, getting something expensive, etc... The players will be required to roleplay that; the GM's role is going to be a simple "yes you can get that" or "no, you need more time/money/work".
As for the idea of a train dungeon... actually... Funny, I just had an idea. Basically, we use the eponymous 'Soul Train' the same way the Persona 4 crew used the television at June's, or how Tartarus functioned in Persona 3. Basically, take the train, ride it to a destination, hop off the train, and then come back when you're done. Just don't take too long or the train moves on without you, and you're stuck in the Shadow/Nightmare world. As the RP progresses and progress is made clearing up the Shadow places, more 'destinations' open up that you can reach by train. Of course, the idea of multiple people entering the train at different times becomes an issue; should there be 'regular trains' to a dungeon, or would the players be in different 'compartments' to represent how they have yet to work together?
It would still be possible to use Personas and fight Shadows/Nightmares in 'Real' Bedford, but that's like Shadows manifesting outside the TV in Persona 4: it's basically Bad News.
On a final note, relationships: While the PCs will inevitably have their own circles of friends and relatives, the whole concept of Persona is that the PCs work together, become friends, maybe even form romantic attachments together. That has to be discussed between the players (naturally), whether through advance planning or just playing it by ear. The GM can offer suggestions, but it's the players who need to find a way to connect.to each other, and to establish a bond over time. How fast the bonds develop is up to the players; whether because two characters work/interact together a lot or because they just naturally hit it off makes it go faster or slower - but it still takes time to turn someone from "perfect stranger" to "my friend till the end".