There are several factors that determine the cross section of a passenger aircraft; the most obvious one is that absolutely nothing is for free - there can be no unjustified weight/surface area/volume/complexity/uncertainty in aircraft design - everything is counted, everything is assigned a priority.
Also obvious is that passengers are higher than they are wide, for logistical purposes.
Then there is that a pressurised vessel composed of the thinnest, lightest, cheapest possible material wants to assume a circular shape.
Less obvious is that passenger aircraft are not built on a keel, or ladder frame, or chassis, or assembled from self-contained modules. The rib & stringer frames you see in aircraft factories are quite fragile & vulnerable until they are skinned - even then they have little strength until final assembly. Fuselages are more like an inflated condom made from postage stamps, rather than a short section of sturdy water pipe. The fuselage has to be many things, bridge, tunnel, pressure vessel, dangerous goods storage, bus, storm shelter, gasworks, auditorium, and always make more money than it costs.
To save weight, & solve as many other engineering problems as possible, the fuselage & floor are designed as a tension structure. Any glance at a cross-sectional diagram will illustrate this, it's easy to imagine a cable holding in the sides instead of floor beams. Of course the floor has to carry vertical loads of passengers & equipment, but that's separate to its contribution to the entire structure.
There really aren't that many double deck aircraft; 747s have a quarterdeck area behind the cockpit that has seating, but that's more a historic quirk, rather than the reason for its success; it was designed as a bar/lounge area. Turning it into limited seating worked because it was, well, limited. The A380 has been a gallant failure,there will be less flying every month. .
A second deck on an aircraft just can't create more problems than it solves. Even when the problems are external to the aircraft - terminals, financing, politics, etc.
If you wanted to have a fuselage wider than it is high, the floor would need to become a heavier compression structure (as pressurisation tries to circularise the fuselage), now subject to bending forces that need to be braced against, adding to structure, adding to weight, adding to cost, depriving space from revenue-earning volume, adding to costs, and so on.
And that's just the floor. You've now changed the shape of the tube you're using to join the tail to the wings & the wings to the nose. You've massively increased the strength of the fuselage in yaw (the least important parameter) while weakening it in pitch (really important), plus probably introducing new, very novel, twisting tendencies into your combination tension/compression structure.
This can be ameliorated by having two circular cross-sections next to each other, instead of a wide ellipse, with the circles overlapping & a vertical wall, or series of posts, or tension members of some sort, running down the length of the cabin.
Part of your sales pitch to the airlines for a very wide cabin was that they could vary whether it was 13 across or 22 across or a flying tapas bar or whatever they desired. Except that now, for the first time, they have an aircraft with a physical divider down the middle.
The regulators also frown on these dividers, because they have tested evacuations from the new triple aisle/quadruple aisle airliner & found that they turn into soccer riots unless entire rows of seats are removed, aisles are doubled in width, emergency exits are doubled in size & number with larger empty spaces around them, supervising cabin crew are increased.
The airlines will not, ever, want an aircraft like that. They want exactly what they have now, but cheaper.
So, we end up with single aisle, circular fuselages and twin aisle, circular fuselages.