I'll outline here some of my preferences and conclusions for design of the Nautilus.  My focus is the exterior, though the layout of course has to influence some design decisions.  Figure 1 is a side elevation; the numbers correspond to the design tour below.

I propose a traditional spindle, with raised platform, pilothouse and light-house, a four-blade propeller with a free-turning rudder forward of it, a lower fin, and some short stabilizers at the tapered end.  Some these features are based on period designs such as the Hunley, and the conclusions of others in the catalog whose designs reflect rewarding thought as well.  

Two big determinations will be discussed in due course: the manner of operation of the pilothouse or wheelhouse, and of the illuminating lantern.  I've followed the implications of the original illustrations, with some interpretations or "clarifications" of my own intended to best reflect "what Aronnax saw" even if the descriptions that have come to us are incomplete.  I provide a vertically retractable wheelhouse at the front of the raised platform, and a triangular-profile lantern aft that retracts like a 1970s car headlight. 

To commence the tour of this Nautilus design:

1. The hull: I opt for a spindle shape, with the 70mx8m dimensions outlined by Nemo.  The hull is capped by a flat platform, has a ramming spur or prong at the bow just above the centerline, and a keel slightly descended at the bottom.  The plates are mostly smooth, but overlap about 2cm where the hull meets the top platform, and the siding of the platform (its top is smooth and flat).
2. The keel, whose weight and dimensions are given by Nemo, would be about 15-16 meters along the bottom of the boat.  I have the keel extend about a quarter meter from the bottom of the hull.  It seems to run slightly forward of the center of the spindle, as I assume (though I am no maritime engineer) the mass of the keel (and the ram) need to counterbalance the mass of the engine room aft.
3. Two movable diving planes are attached along the centerline on each side of the hull, measuring about 3mx2m and positioned just slightly forward of amidships.  In front of these movable planes are two small canards or winglets, to protect the planes from fouling and shock on impact.  
4. The Salon window: I place the Salon forward of the pilothouse, and follow most of the designs on the Nautilus page.  The window is an oblong with rounded corners.  Above the window is another floodlight (unnoticed by Aronnax, who assumed the light came from the lighthouse).     
5. The diving hatch door is positioned approximately below the lighthouse, as a beacon to returning explorers.  Probably the opposite side of the diving chamber is a larger door to haul in the richest the seas.  
6. The propeller has four blades and a sturdy point on the hub, which extends about a meter past the propeller, as we are told the Nautilus reversed at speed to break out of the ice from this end.  I ultimately did not provide a ring or other enclosing protection around the screw, though there is merit to the debate and the example of the Goff Nautilus and the Hunley.  I concluded however that any protective structure would have to be so massive (as in some designs) as to completely obscure the propeller, but that is not what Aronnax saw.  Slighter protection would merely become smashed and tangled in the Nautilus' attack. Possibly the best studied example of the type of attacks the Nautilus made - steel ramming a wooden ship - is ironically the ramming of PT-109 by the IJN Amagiri in 1943, in waters the Nautilus passed by en route to Vanikoro.  Kennedy's wooden PT-109 was sliced in two by the Amagiri and sank in two sections (forward floating for several days).  The Amagiri however was damaged even in this unequal contest: its starboard rudder was bent and affected the running of the ship.  This example, plus the three attacks recounted in 20kL (grazing the Lincoln, the mysterious attack during Aegri Somnia, and the Hecatomb attack), show the Nautilus too suffered damage at least a third of the time.  It was a hazardous means of attack.  In any case, I have mostly left the propeller free, and assume the Nautilus carries a few spare blades!
7. The rudder, following Gagneux, is a freely turning, center-post rudder forward of the propeller.
8. Bottom stabilizer: this fin is provided as a result of several conclusions. It provides some anti-fouling protection to the rudder and propeller.  Also by being as deep as the keel of the Nautilus, it can serve as a resting-fin for the numerous occasions the Nautilus is described as resting on the ocean floor.  Various measuring devices could be attached to this as well as other designs have provided.  
9. Vertical stabilizer: while not so high as to noticeably break the surface, the vertical stabilizer steadies the Nautilus and provides some protection to the propeller.  As other designs have found, this is a useful addition and Nemo might have added it after the first sea trials himself!
10. The ram is one of themes important obscure features of the boat.  Usually described as a spur, never as a spear, but once as a lightning-rod in the storms of the Atlantic, I ultimately added a prong of about 3m, with reinforces flanges in a capital "Y" shape.  After considering a variety of knife-edge and chisel-tip designs, such as used by the Confederate ironclad ram Virginia, I concluded that the ram had to be a sturdy, somewhat vertically elongated prong to punch open a ship's hull (or wretched cachalot or orca body).  We know it left a triangular impression in the Scotia, hence the triangular pattern flanges.  A long spear such as that of the Plongeur would be too delicate.  The ram could not be too elaborate or extended to attach to the hull, given the separate construction of various components.  

11. The platform is some 28 meters long, of parallel sides and pointed front and back at a 108-degree angle, the angle of a regular pentagon.  The sides are angled at about 36-degree.  The platform is about 3m wide (4m at its base meeting the hull).  The platform has retractable poles for a rope balustrade along the sides.  While the top surface of the platform is flat, the iron plates along the edging of the platform overlap slightly, as do the first ring of plates meeting the platform on the hull.  
12. The sealed longboat, sitting upright in its hull recess, rises about half meter above the platform; aft of the boat is the main hatch.  There could be another hatch aft of the lighthouse.
13. The pilothouse: Because of the practical demands for a functioning base of navigation, the explicit need for the housing to retract into the hull and still function, and the unclear descriptions and depictions of this compartment, the wheelhouse presents altogether some of the most vexed questions about the design of the Nautilus.  Indeed it may be that when a satisfactory explanation and depiction of the wheelhouse is reached, the rest of the design flows into place around it.  My conclusions are intended to present the most practical range of solutions.  I opted for a regular pentagon, of vertical sides, two meters high with the top meter normally rising above the platform, with the two forward angled sides raked back 36 degrees for the top meter of height.  The cabin has portholes in all five sides, but whenever the light is engaged, the rear window is automatically closed (indeed the first action of engaging the light would be to trigger the rear window closure so as not to blind the occupants).  I see this cover as a spring-loaded mechanism sliding from bottom to top to cover the rear porthole.  It is true Aronnax, inside the pilothouse, saw four portholes.  But someone standing in front of one wall with a closed-off window behind, and seeing four other walls around with portholes, may write that they were in a four-sided chamber.  The pilothouse is reached from the back through a narrow hatch up a few steps.  When retracted the hatch is narrower still.  When clearing the decks for action, the pilothouse is pushed down to be flush with the platform.  The three back flat sides slide smoothly into the platform. The front of the wheelhouse becomes the front of the platform, with the two forward windows forming the 36-degree raked angle leading edge.

14. If the wheelhouse is the most contentious part of the design, the lantern housing may be one of the most complex subcomponents of the Nautilus, because of its variable position,  brilliant light, and multiple lenses and mirrors. The light is actually depicted fairly consistently in the illustrations: a triangular housing casting a wide beam forward. To this we have to add times when the light is the center, not the base, of a brilliant oval light.  The light house, rising a bit higher than a meter, is an equilateral triangle with flat forward and rear faces.  A large lens faces forward and two slightly smaller lenses are on the sides. The lifting mechanism lies not in this triangle but forward of the housing in the hull at about 30 degrees from vertical.  The triangle contains additional movable lenses and mirrors to adjust the direction of the light.  The housing is retractable, along both its forward and rear bases. Hinged at the back, the large forward lens retracts safely into the platform.  When hinged at the front, the large lens points straight up, to create a mysterious phosphorescent glow and to illuminate spaces such as inside the coalmine volcano.