I figured the real innovation in the Prometheus design was in the software, not the hardware, so to speak.
Basically it lets one commander and bridge crew control a small fleet from one central bridge, directly, without going through intermediaries. Presumably the bridge of the primary module of the Prometheus is set up to provide easy access and control of the other two parts. The tactical station is set up to allow one tactical officer the ability to swiftly change battle plans for all three ships, the sensors set up to utilise triangulation or such from being able to scan from three different points, the helm allowing a pilot to guide the ships in formation and so forth.
Technically the same thing can be accomplished with a squad of three ships, each with their own crew, or a mothership with two smaller vessels. But the Prometheus is set up to do this more efficiently (and with fewer officers).
As for cloaking, the Mass Effect PC game deals with heat build up in ships quite heavily in it's universe and posits some ideas on how cloaks could work:
Basically it lets one commander and bridge crew control a small fleet from one central bridge, directly, without going through intermediaries. Presumably the bridge of the primary module of the Prometheus is set up to provide easy access and control of the other two parts. The tactical station is set up to allow one tactical officer the ability to swiftly change battle plans for all three ships, the sensors set up to utilise triangulation or such from being able to scan from three different points, the helm allowing a pilot to guide the ships in formation and so forth.
Technically the same thing can be accomplished with a squad of three ships, each with their own crew, or a mothership with two smaller vessels. But the Prometheus is set up to do this more efficiently (and with fewer officers).
As for cloaking, the Mass Effect PC game deals with heat build up in ships quite heavily in it's universe and posits some ideas on how cloaks could work:
For most ships, the heat generated through standard operations is easily detectable against the absolute-zero background of space. The Normandy, however, is able to temporarily sink this heat within the hull. Combined with refrigeration of the exterior hull, the ship can travel undetected for hours, or drift passively for days of covert observation. This is not without risk. The stored heat must eventually be radiated, or it will build to levels capable of cooking the crew alive.