Okay, Guess I'll do this in order:
4 nacelles, lets see, I see it as what the Navy does. The navy's fighter planes all have 2 engines, why? So if 1 goes out over the ocean, yu have a back up to get back to the ship. So in my head, 4 nacelles is for redundancy for long range ships. If something goes tits up and you loose 1 nacelle, you still have 3 to get you home. You might even cannibalize bigger components from a dormant nacelle. As mentioned you could run 2 nacelles for a long period of time, and then switch out to the others. Things break, things wear out.
Homosapiens only club:
Well it is a tv series with limited budgets, so thats the #1 point. However, lets say that its is a majority human starfleet, atleast in the 23rd century. Humans could be more brash, more optomistic, more interested in exploration than the other species, Were the new kids on the block in that most of the other speicis have had warp travel for awhile, and they already have there colonies, explored whats in there neighborhood. So to me, Humans want to be out there, want to push the limits, but other speices, as a mostly whole, have there own wants and needs, and maybe exploration isn't a big thing to them. They do have people that volunteer to go in to starfleet, but not as much as a % as humans do. So to me it might be a 75% human to %25 alien crew on most ships. Over time more speices are added, and the % of humans goes down by the 34th century. But I see that Humans take being in the federation seriously, and is something worthy to strive for to be in starfleet, where say Vulcan, its seen as a thing that is "Beneath" them, like some people that see the military as a bunch of poor people with nothing better to do in there life, the better thing is to go to collage etc. Thats why Spock going in to starfleet was seen as a waste.
Now the Expeditionary fleet, to me, as said, other species have there own priorities, and maybe starfleet doesn't jive with them, so they do have there own fleets, for exploration, for passenger service, for cargo hauling. So as an example, Vulcan wants to go to some star 50 ly away to study something, starfleet says, sorry we're busy, or we're over here right now. So vulcan sends its own ships out to study, its like woods hole oceanographic, its a civilian thing that does its own stuff. I've never seen starfleet as the end all for exploration needs.