What are the issues with building modular aircraft?
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.