Basically, the ship is now actually 6 component ships. The saucer section is still the largest and holds most of the crew - and a sizable garden area for recreation and hydroponics (using matter/energy transmission to manipulate stuff is really wasteful from an energy perspective, and gardens are good for moral.) The "column" of the ship is the Battleship, which has the shields, anti-matter torpedoes, phaser bays and primary reactor.
There are two CICs - the civilian and military. I figure that Starfleet should be split into a merchant marine, military, diplomatic and survey branches (since specialization increases efficiency.) Since the Enterprise D handles three major things (military, diplomatic and survey branches) I figure that the ship would have three integrated crews, with a science team and diplomatic core that is organized and protected by the military branch.
|The Enterprise D|
Each Exploration pod is basically a small bridge that can hold a few dudes, a single phaser, a shield generator, and a MASSIVE cargo bay to take samples and be refitted. If there is diplomacy, the cargo bay is reordered into a diplomatic suite. If there is combat, it can be loaded with anti-matter torpedoes. If they need to do major construction, it can ferry supplies (or refugees, for that matter.) If the primary ship is damaged, the saucer section can be evacuated into the exploration pods, and they can scatter, increasing the chance that at least some people will get away.
With this design, the science teams (not trained for away missions, obviously) can focus their time on researching samples brought back by the multiple, simultaneous away missions run by the 4 pods. The battleship can be used if anyone threatens the ship, or as added power for exploration - and, because it always has the warp engine, it can rapidly respond to emergencies.
I have too much time on my hands.