This might make sense as
Designing "better", upgraded part is a lot of work. And then everything has to be thoroughly tested to work together, which is even more work. That's why aircraft manufacturers usually choose to upgrade as few parts as possible and only those where most significant benefit is expected.
Take for example 737. The type was upgraded with new engines several times, because evolution in engine technology brought significant fuel savings. But the wings only got winglets, which was less work than redesigning the wing. And the fuselage was not changed at all, only it is now built longer by adding some frames.
And the situation with A320 is similar. The "NEO" designation for the new series entering production stands for "new engine option", because that's what the upgrade is about. Beyond new engines and winglets there is basically no other change.
And that was just type changes as in new aircraft being built from upgraded parts. Upgrading an existing airframe is another can of worms.
Basically the joins between airframe components have to be very strong and light. The most common joining method that satisfies this is riveting, with gluing gaining popularity for composites and in some cases welding appears (aluminium is difficult to weld, but friction-stir welding seems to work satisfactorily).
Well, none of these methods allows easy disassembly. To make the components replaceable, they would have to be bolted instead. However, bolts have several major disadvantages. They can shake loose, they don't fit tightly (rivets expand to fit) and they are considerably heavier. These things make them totally unsuitable for the high-stress joining, especially for joining fuselage and wings. And drilling out the rivets and riveting in a replacement is too much work and there is a high risk of damaging the parts, which could easily make them unsafe to use.
And then there is a question of the removed parts. So you replace the wings after half of their life, because new, more efficient model is available. But the old wings could have still generated revenue. By discarding them, you've lost those money. So to pay off, the difference in efficiency must make up for that.
Well, it is extremely unlikely to do so. The new engines of 737MAX or A320NEO save about 15% of fuel, but engines are the component where by far largest benefit could be gained. Redesigning any other component can save at most few percent.
Yes, some airframes did get structural upgrades (upgrading avionics or other small components is of course easier and thus done more often), but usually these were military aircraft where the changes provided some other benefit that was worth the effort.
And some more airframes got refitted to different engines, but engines have shorter life, so they have to be designed to be replaceable. And even there it is usually military aircraft and usually only because the airframes are used much longer. For example KC-135 was reengined, but that was about the time its civilian counterpart, B707, was scrapped altogether.
But most of the time, replacing parts of an aircraft would not prevent any wastage but rather create a lot of it.
Upgrading most of the items listed in the question would be considered a major change, and require approval from regulators. For an example let's just consider wings, nose, tail, engine, and fuselage. That's 5 different major sections of the plane. Even if there are only 2 options for each of those, that creates 32 unique configurations. Even if some of these can be eliminated, this is a lot of configurations. Each one would have to be approved by regulators. The manufacturers would also have to stock parts for the different options, reducing the benefit of designing, manufacturing, and installing a larger number of just one part.
There is good reason for having every major configuration separately certificated. Airplanes, especially airliners, are complex machines, where all of the parts interact in many ways that affect the performance and safety of the aircraft. It takes a lot of analysis and testing to fully understand all of the interactions and ensure the aircraft will perform as expected.
This being said, some options do have enough demand to be offered by manufacturers. Most aircraft have different fuselage options that vary in length, allowing different passenger capacities to match the needs of operators. However, cutting into the fuselage to change this would be much more expensive than just selling the plane and buying the desired size. Many aircraft also offer engine options from different manufacturers. Although compatibility is generally limited to one engine type, engines can be removed with relative ease and performance upgrades can be available. Although avionics are typically standard, there are upgrade options as newer technologies emerge. Seats are already a modular component that can be rearranged and swapped out and are generally chosen by each airline.
Wings must carry the full load of the plane, and often integrate engines, landing gear, and fuel tanks. They tend to be more efficient with a larger span but aircraft are also limited in wing span, so even different sizes of the same type may use the same wings. Adding winglets is an option that requires much less work than replacing the whole wing for a small improvement in performance.
There can be different options associated with landing gear, such as different types of brakes or tire pressure monitoring. Other than that, there aren't many options to be offered. Landing gear does have a hard limit on lifespan though, so it is designed to be replaceable.
The tail tends to be designed and sized to the aircraft, and is critical for aircraft stability and control, so is typically the same across versions of a model.
As far as offering upgrades to major components, the benefits of such an upgrade usually do not outweigh the large costs of offering it.
One reason that aircraft aren't modular is that many aspects of aircraft design are done looking at the whole airplane, not just at its parts. Some examples are:
That being said, things that can be added or removed easily like entire avionics platforms, wingtips, seats, or sensors sometimes are, as noted in fooot's answer. The modularity of an aircraft is more like building and less like a desktop computer.
The centre of gravity of an assembled and loaded plane must be in the right position, relative to the position where the wings are connected. Fitting a different tail, nosegear, engines would affect the fore and aft position of the cg.
Therefore we would need a fuselage where the wing position could be varied according to the chosen configuration.
Problem: the fuselage needs to be as light as possible in most places, and strengthened in the place where the wings are connected. So we would end up needing a different fuselage for every configuration.
(There are many other reasons why a totally flexible modular approach is impractical, but I've given the most basic engineering-based one I can think of.)
