On the timeline thing: I have my own theories for how to reconcile the "overwriting history" model with the Many Worlds model, but it's all too complicated and niggly, and the
really right explanation is:
Don't worry about it. Time travel follows whatever rules best serve the story. It's ultimately a fantasy conceit; by real physics, you probably couldn't travel through time anyway, and if you could, you'd be compelled to re-enact your existing timeline and could never enter another one. So it's just a device for telling a tale. If the story needs it to work a certain way, then that's how it works. Just accept that and the headache will go away.
Star Trek has had plenty of interesting characters on Federation ships who weren't members of Starfleet. Guinan, Kes, Neelix, Seven of Nine, the Maquis, T'Pol... Personally, I think it gets a bit cliche when the cast can be defined by their positions - engineer, doctor, helmsman, etc. I see no problem with having other non-Feds as characters.
All those people served purposes aboard the ship. B-4 is a toddler. Or perhaps a better analogy is an adult with a severe learning disability. Not only can he contribute nothing aboard a starship, but a starship is not a safe or constructive environment for him. It makes much more sense for him to be under the care of the Daystrom Institute.
As a side point: you seem to be using "Federation" and "Starfleet" interchangeably, which is a tendency that troubles me. They're not synonyms any more than "United States" and "US Navy" are synonyms. Starfleet is an organization that serves the United Federation of Planets. Most people in the Federation have nothing whatsoever to do with Starfleet. I never said anything about whether B-4 is a Federation citizen; indeed, by the Federation Council ruling of October 2380, I'd say he is. But just because someone's a Federation citizen doesn't mean there's a good reason for him to serve aboard a Starfleet ship of the line, any more than just being a United States citizen is a good reason for someone to take up space aboard a Navy aircraft carrier.
And I beg to differ on the 'B-4 is not family' argument. He was Data's brother as much as it's possible for him to have a brother... or at the very least, his semi-retarded cousin.
Valid from a sentimental standpoint, but not from a practical standpoint. Data is no longer a member of the
Enterprise crew. Therefore, B-4 is not technically or legally a family member of anyone aboard. Again, B-4 is functionally a child. Imagine if Miles and Keiko O'Brien had died rather than leaving for DS9. Would you have argued that their baby daughter should've been kept aboard the
Enterprise, rather than sent off to live with her grandparents?
I find the "he reminded the crew too much of Data so they decided to get rid of him" angle a bit harsh.
Did anyone ever say that happened? They were ordered to disassemble B-4 and deliver him to the Daystrom Institute -- and it's worth noting that he was kept onboard for five whole months before that happened. Now, in
Greater Than the Sum, Geordi did express the opinion that he didn't fight hard enough to stop it because he'd grown frustrated with B-4's failure to be like Data, but that was guilt speaking as much as anything, and it's not the same as "decid[ing] to get rid of him."
I think the opposite angle could have been played up well - say for example, Geordi wanting desperately for B-4 to fill a part of Data's shoes that he's just not capable of.
That's pretty much why Geordi kept him around for those five months between
Nemesis and
Resistance, trying to bring out some glimmer of something Data-like, without success.
Something I'm curious about: Looking at the new movie's explanation of time travel and coexisting timelines as a model, did the Borg and the crew of the Enterprise-E create a divergent timeline when they travelled back to 2063 in First Contact? And what about the Temporal Cold War on Enterprise that led to, among other things, the Xindi devastating Earth in the 22nd century? If the new movie is anything to go by, this means there were already a couple of different realities branching off from one another before Nero came along!
More than a couple. See "Parallels." There are millions, at least. The number of potential alternate timelines arising from either time travel or spontaneous quantum divergence is unbounded (which doesn't mean infinite -- just that there's no limit on how many there
could be).
One question though, when the Enterprise disappeared at the end of First Contact, did they go back to their home 24th century, or did they end up in the 24th century of the new timeline they'd just created?
Logically, they'd end up in a new timeline very similar to their old one. But dramatically, it's always assumed to be the same one. I rationalize this by assuming that if two timelines are similar enough, they can merge together into one.