Around here we have a highway tunnel under a river that has watertight doors in case the river floods: if the water rises high enough to flood the tunnel, they close the doors and wait for the flood to subside.Sojourner, i think your overestimating the amount of maintenance the Prometheus will need. Sure it's maintenance will be higher than normal for a ship it size, but I'm pretty sure that is not a big problem. I hope we all are thinking the bulk of the maintenance on the Prometheus will be due to it's MVAM. I don't really see that as a problem as starfleet clearly make it a practice to use predictive maintenance (http://en.wikipedia.org/wiki/Predictive_maintenance). I don't imagine that MVAM will be used very often, so there is no real need to do constant maintenance on it. That would just be a waste of time and labour.
They would check the motor that moves the doors to make sure it was working a couple of times a year (maintenance on that motor), but decided not to check the actual doors themselves since doing so would require closing the tunnel to traffic for about an hour.
A few years ago we had a hurricane hit us, and the guys who were sent to close that door discovered that the door would not set into position properly because some of the parts were jammed with decades of grit. They kept trying, and nearly lost their lives trying to get that door closed (they were rescued, but the current swept their truck down into the tunnel). It took weeks to pump the water out, then to clean the debris and check for damage.
Any system that has moving parts needs maintenance, whether it is being used or not. Often not being used is worse than being used, as it lets little problems turn into big ones without being noticed.
I agree that a science ship will have a different crew than a warfighter, but that all balances out: the Prometheus probably carries the same crew compliment as any ship of similar size with a similar role. And the same crew could be distributed among three smaller ships, either each capable of all the same mission or separated into specialist ships. The reason to build the bigger ship is that it costs less, and does some things more efficiently. But if you build a big ship that can split into three (which is the same as three small ships that can merge into one), it not only doesn't cost less, it costs more. You need to derive a major benefit to make it worthwhile.
And I did not mean to suggest that I thought that only one section of the Prometheus carried crew. Others had expressed that possibility, and I agree it is possible. I wanted to point out that it changes nothing: the ship needs the crew it needs, and it doesn't matter to the overall ship if all of their quarters are in one place or not.