If I was going to re-design the Prometheus, I would makes sure that, if one (or more in the case of the 5-ship version) parts were destroyed, the remaining parts could still recombine. With the version used in the show, the top "command" module looks like it can only combine with the top "drone", and not the bottom "drone"...and if the top component was destroyed in battle (which could very well happen in a fight) the two remaining components couldn't re-combine.
And in my version I'd make each of the 3, 4, or 5 (or whatever) components were the same as the others, and each capable of operating independently...because if you have a "command" module and some slaved "drones", and the command module was destroyed...that would suck. The only complication with that design is, as pointed out with the linked-to article, is that each component would have to have it's own copy of everything...warp core, sickbay, cargo and engines and fuel storage and transporters.
Or you could just have a large Galactica or Andromeda type carrier and multiple smaller drones. Maybe even a medium-sized carrier with 5 or more smaller attacher "rider" type drones, so that if any and even all were lost...the mothership could continue on. (And if the drones were truley un-manned, it wouldn't matter if the mothership carrier was lost, no one would be stranded. Or the drones could be piloted be on-board strong AI's with small warp-cores so that they could return to a base if the mother carrier was lost.